File System Corruption Recovery: Causes, Tools & Complete Guide

File system corruption can appear seemingly out of nowhere, and when it does, it can lock file access, show confusing error messages, or even make your drive unreadable.

Whether it’s a result of corrupted partitions, RAW drives, or other system faults, if you’re seeing error messages like “The file or directory is corrupted and unreadable,” it is most likely a sign of file system corruption. This can result in permanent data loss if not handled properly.

In this guide, we’ll tell you everything you need to know about file system corruption recovery and also give you helpful tips to identify warning signs early. We’ll also cover the best tools (both built-in and third-party) that can help you recover data after file system corruption and restore your storage device to a working condition.

What Is File System Corruption

File system corruption occurs when the directory structure that keeps track of your files and folders becomes damaged or unreadable. Think of it as losing the table of contents or index of a book; your data may still be present, but the system no longer knows where or how to access it!

Every operating system uses a file system. The common ones for Windows include NTFS, FAT32, and exFAT, while macOS uses APFS or HFS+. These structures essentially help you to organize, retrieve, and manage your data. So when these structures become corrupted, it can result in your files missing, drives turning RAW, or the system refusing to boot at all.

Corruption can either affect a part of the file system (like metadata or allocation tables) or it might render the entire partition unreadable. Either way, if you ignore some of the early warning signs, things tend to snowball quickly, leading to possible data loss or complete drive failure. So, let’s try and understand some of the common causes of file system errors.

What Causes File System Errors

Even though it may seem random, file system corruption isn’t random and usually stems from preventable hardware or software faults on your device. Here are some of the most common triggers.

• ⚡ Sudden Shutdowns or Power Loss: Abrupt power failures can interrupt critical read/write operations on your drive. If the system is in the middle of writing to the file system when power cuts out, it can sometimes lead to incomplete or inconsistent data structures, resulting in file system corruption.
• 💽 Faulty Storage Devices: Drives nearing end-of-life or those with manufacturing defects may struggle to maintain your data’s integrity. Mechanical issues in your HDDs or degraded NAND cells in your SSDs can cause corruption in the metadata or even wipe out entire sections of the file system and cause corruption.
• 🛡️ Virus/Malware Attacks: Some malware specifically targets system files or boot sectors, and can alter file permissions, encrypt structures, or even delete important bits of metadata. Even non-targeted infections can cause instability and trigger cascading errors in your PC or drive’s file system.
• 🔁 Bad Sectors: When sectors on your drive go bad, the system can fail to read or write data correctly. If these sectors are part of the file system’s control areas (for example, the Master File Table in NTFS), it can result in unreadable partitions or file loss.
• 💥 OS Crashes or Driver Conflicts: Low-level system crashes that occur during disk operations (especially involving buggy or incompatible storage drivers) can corrupt file system structures on your device. If you recall seeing repeated blue screen of death (BSOD) errors or system freezes, this can point to underlying I/O instability and explain why you’re having file system errors.
• 🔌 Improper Removal of External Drives: Yanking out that USB drive or external hard disk without ejecting it first can interrupt important buffered write processes. This can leave the file system in something called a “dirty” state, especially in FAT32 or exFAT systems, which are used commonly in portable storage devices.

How to Detect File System Corruption

1. CHKDSK and S.M.A.R.T. Tools

CHKDSK is a built-in Windows utility that checks your disk’s integrity at the file system level. Running chkdsk C: /f makes your system try and fix logical errors, while chkdsk C: /r scans for physical bad sectors. If CHKDSK frequently flags index errors, lost clusters, or cross-linked files, it could be a sign that your file system is deteriorating.

On the hardware side, S.M.A.R.T. attributes reported by your hard drive can be accessed by tools like CrystalDiskInfo or Speccy. They are used to monitor metrics such as reallocated sector count, CRC errors, and spin-up times. A sudden drop in these health indicators usually signals impending drive failure, which often results in file system corruption.

2. File Explorer Errors

When your file system is damaged, Windows may not be able to map your file structures correctly. This results in odd behavior in your File Explorer—you might see files appearing as blank, folders vanishing, or drives showing you errors like “Access Denied” or “You need to format the disk before use.”

Additionally, files might open but display garbled content or refuse to open at all. Even renaming a file or copying data might throw up cyclic redundancy check (CRC) errors. If you’re experiencing any of these, there’s a good chance that the underlying file system has problems.

3. Disk Management warnings

Launching the Disk Management console (by running diskmgmt.msc in Windows + R) lets you take a deeper look at your drives. A file system corruption issue will present itself here as a drive labeled “RAW,” which means your system can’t recognize the existing file structure.

You may also see mismatched capacity reporting, like 0 GB used/free space, or partitions being marked as “Unallocated” in Disk Management. If the disk status reads “Healthy (At Risk),” that’s a red flag for sure. It means that the structural or mechanical issues tied to the file system might lead to corruption.

How to Fix File System Errors Using Windows Built-In Tools

1. Use CHKDSK to Fix File System Corruption

As we discussed above, CHKDSK is a Windows utility for scanning and repairing file system errors in your hard drive. This utility can potentially fix logical errors within your drive, which can improve file system corruption symptoms.

⚠️Note: Always proceed with caution since CHKDSK can inadvertently overwrite your data and lead to data loss. Before using this tool, always back up your files.

Here’s a simple guide on how to use CHKDSK to scan and fix file system errors.

1. Open File Explorer on your system, and click on This PC. Now right-click on the drive on which you’re facing file system errors.
2. Select Properties and then navigate to the Tools
3. Under the Error checking section, click on Check. This starts the scan, and CHKDSK will now check your drive for file system errors.

4. Click Scan drive on the window that pops up. If any errors are found, you can choose to fix them with the options shown.

Note: CHKDSK can only repair soft bad sectors, which are commonly seen in internal drives. If your hard drive has hard bad sectors (like in external drives due to mechanical damage), CHKDSK simply marks them as unusable.

2. Use SFC /scannow to Fix File System Corruption

Corrupt system files can cause BSOD errors, among other problems, and you can repair them using Windows’ built-in System File Checker (SFC) tool, which scans and repairs file systems automatically. Here’s how to use SFC /scannow.

1. Type cmd in your Windows search bar and right-click the Command Prompt Now select Run as administrator.
   
2. In the command window, type: sfc/scannow and press Enter.
   

3. Wait for the scan to complete (can take anywhere between a few minutes and an hour, depending on the size of your disk.

3. Use DISM to Fix File System Corruption

If using System File Checker doesn’t fix your issue, try the Deployment Image Servicing and Management (DISM) tool. It can repair deeper system corruption. Here’s how to go about using DISM.

1. Once again, open the Command Prompt and run it as an administrator.
2. Type the following command: DISM/Online/Cleanup-Image/RestoreHealth

3. Press Enter and wait for the process to complete (it took our PC about 10 minutes to run this command).
4. Now restart your PC and check if the problem still persists.

File System Recovery Using Stellar Data Recovery

When CHKDSK, SFC, or DISM can’t fix your problem, or if they fail to access your data entirely, Stellar Data Recovery for Windows offers a robust fallback. It bypasses OS-level failures to extract your files safely from severely corrupted file systems or even unreadable drives. Some of its features include:

• 🔍 Preview Before Recovery: One of Stellar’s standout features is its ability to show you recoverable files in a tree hierarchy before you commit to recovery or buy a license. This helps you verify the integrity of your data and prioritize what matters to you.
• 🧮 File System Support: Stellar Data Recovery software supports a wide range of file systems beyond just NTFS and FAT, such as:
  • Windows: NTFS, FAT32, exFAT
  • macOS: HFS, HFS+, APFS
  • Linux: ext2, ext3, ext4

You can use Stellar when your:

✅ File system is RAW or inaccessible.

✅ You see error messages like “Drive needs to be formatted.”

✅ Built-in tools crash or stall.

✅ You need to recover deleted or partially overwritten files.

Stellar Data Recovery software is beginner-friendly, so you can use it in just a few clicks, yet powerful enough for IT admins!

Tips to Prevent File System Corruption

Here are handy tips we’ve found that work best to help prevent file system corruption in the first place.

• 📦 Regular Backups: Use external drives or cloud storage to routinely back up important data. Scheduled backups reduce your risk of data loss in case of drive failure or accidental deletion.
• ⚡ Use Surge Protectors: Power surges and sudden outages can interrupt disk writes, leading to corruption. A surge protector or UPS can help you avoid this.
• 🧩 Avoid Unsafe Drive Ejections: Always use the “Safely Remove Hardware” option before you unplug USB drives or external HDDs to prevent incomplete write operations.
• 🛠️ Monitor Disk Health Regularly: This tip might be a little harder to commit to, but using tools like CrystalDiskInfo or built-in M.A.R.T. monitoring can alert you to a failing drive before it’s too late.
• 💾 Format Drives Correctly for OS Use: Always use the recommended file system for your operating system. For example, NTFS for Windows, APFS for modern macOS, and exFAT for cross-platform compatibility.

Final Verdict

File system corruption can start with minor glitches and then escalate into a complete data lockout if you leave it unchecked. While Windows offers useful tools like CHKDSK and SFC to detect and fix many of these early issues, they don’t always work, and they can’t recover your files, especially if the drive has physical damage or logical corruption.

That’s where Stellar Data Recovery comes in. It provides you with a safe, reliable method to extract files from even RAW or unreadable partitions, supports multiple file systems across platforms, and offers a preview-before-recovery option so you know exactly what you’re getting.

So don’t wait for a warning sign. Back up your data regularly, monitor your drives, and keep Stellar in your toolkit to always be prepared!

FAQs

1. Can CHKDSK fix all file system issues?

No. CHKDSK handles many logical errors but cannot recover lost data or fix physical damage on your drive.

2. Can Stellar recover files from RAW partitions?

Yes. Stellar Data Recovery can scan RAW drives and recover files even if Windows prompts you to format the drive.

3. What file systems does Stellar support?

Stellar supports NTFS, FAT32, exFAT (Windows); HFS, HFS+, APFS (macOS); and ext2/3/4 (Linux).

4. Can I use Stellar to recover only selected files?

Yes. After scanning, you can preview and choose specific files or folders for recovery, thus saving both time and space.