How to Clone a Drive with DiskGenius

DiskGenius is a partition manager that also clones disks and partitions. The free edition can copy partitions, while the paid Professional edition adds system disk cloning and boot repair. DiskGenius supports file-based and sector-by-sector modes, and it can skip bad sectors during the copy.

This guide explains the DiskGenius clone modes, its limits on the free edition, and when you should switch to a more guided tool such as Qiling Disk Master.

DiskGenius Clone Modes

File-based clone. Also called intelligent clone, it copies only used sectors and skips empty space to save time.
Sector-by-sector clone. Copies every sector exactly, including empty and damaged ones, which is required for non-Windows file systems.
Bad sector skipping. DiskGenius can retry and then skip unreadable sectors so the clone continues instead of failing.
GPT and MBR support. The tool can clone disks with either partition style and preserve the boot structure.
4K alignment. DiskGenius can align target partitions to 4K boundaries when creating them on an SSD.

Choose file-based clone for Windows system disks and sector-by-sector clone when the source contains a file system DiskGenius does not understand, such as a console or Linux setup.

DiskGenius main window showing the disk and partition list

Limits of the Free Edition

No system disk clone. The free edition cannot clone the Windows system disk; only partition cloning is allowed.
Boot repair is paid. Rebuilding the EFI and BCD after a system clone requires the Professional edition.
No incremental clone. DiskGenius does not support incremental or differential cloning, only full copies.
Manual partition work. You often need to create target partitions yourself before copying data into them.
Fewer guided features. The free edition lacks one-click system migration and automatic boot fixing.

For a simple data partition copy the free edition is enough. For a system disk clone that must boot, the Professional edition or a guided alternative is required.

Selecting the destination partition in DiskGenius

Prepare Disks for a DiskGenius Clone

Back up the target. Cloning wipes the destination disk, so move any data off it first.
Match the partition style. Decide whether the target will be GPT or MBR before you start the copy.
Create target partitions. In the free edition you may need to create equal or larger partitions on the destination.
Run a disk check. Run chkdsk on the source so the file system is clean before cloning.
Disable fast startup. Turn off Windows fast startup to avoid a locked source volume.

Do not interrupt the clone once it starts. A partial copy leaves the target unbootable and may require reformatting to try again.

Clone with Qiling Disk Master

Because DiskGenius Free cannot clone the system disk, many users switch to Qiling Disk Master for a one-click system migration that aligns 4K sectors and rebuilds the boot records automatically.

Watch the video tutorial below to clone the drive step by step with Qiling Disk Master.

Free Download
Windows 11/10/8/7, 100% Secure

Step 1. Open Qiling Disk Master, choose Clone, and then select Disk Clone.

Choose Disk Clone in Qiling Disk Master

Step 2. Select the source disk and click Next.

Select the source disk

Step 3. Select the destination disk and confirm that its data will be replaced.

Select the destination SSD

Step 4. Enable SSD alignment and choose intelligent clone to skip empty sectors.

Choose the clone mode and review the partition letters

Step 5. Click Proceed, wait for the copy to finish, then shut down before changing the boot order.

Monitor the clone progress bar until the task finishes

Repair Boot After a DiskGenius Clone

Boot from Windows install USB. Choose Repair your computer to reach the recovery menu.
Open Command Prompt. Use Troubleshoot, Advanced options, then Command Prompt.
Rebuild the BCD. Run bootrec /fixmbr, /fixboot, and /rebuildbcd to restore boot records.
Fix the EFI partition. Assign a letter to the EFI volume and run bcdboot C:\Windows to rebuild boot files.
Use Startup Repair. The automatic repair option can fix common boot issues without typing commands.

If the cloned disk still will not boot, the partition style or the EFI partition may not match the firmware. Convert the target to GPT for UEFI or MBR for Legacy BIOS and clone again.

FAQs About Cloning with DiskGenius

Can DiskGenius Free clone the Windows system disk?

No. The free edition supports partition cloning only. System disk cloning and boot repair require the paid Professional edition.

What is the difference between file-based and sector-by-sector clone?

File-based clone copies only used sectors and is faster. Sector-by-sector clone copies every byte exactly and is needed for unknown or damaged file systems.

Does DiskGenius skip bad sectors during cloning?

Yes. DiskGenius can retry and then skip unreadable sectors so the clone continues, though files on those sectors will be corrupted.

Will DiskGenius align my SSD at 4K?

Yes, when you create target partitions you can enable 4K alignment. Verify the alignment afterwards with msinfo32 if needed.

Does DiskGenius support incremental cloning?

No. DiskGenius only does full clones. For incremental images use a backup tool instead of a clone operation.

Back Up Before You Clone

Cloning overwrites the target and can fail on a source with bad sectors. Back up Windows first so you can restore if the DiskGenius clone leaves the disk unbootable.

Watch the video tutorial below to back up Windows and restore it if the clone fails.

Free Download
Windows 11/10/8/7, 100% Secure

Step 1. Open Qiling Disk Master and select System Backup to include the boot partitions.

Select System Backup in Qiling Disk Master

Step 2. Save the image to a drive other than the target and start the backup.

Choose a folder on another drive for the system image

Step 3. Click Proceed to start the system backup and wait patiently until it finishes. You can also tick Shut down the computer when the operation is completed to power off automatically.

Watch the system backup progress until it finishes

Step 4. If the cloned disk does not boot, restore the system image and rebuild the BCD from Windows Recovery.

Restore the image with Disk recovery when the clone fails

Conclusion

DiskGenius clones partitions and disks with file-based or sector-by-sector modes and can skip bad sectors. The free edition cannot clone the system disk or repair the boot, so for a bootable Windows migration use the Professional edition or a guided tool like Qiling Disk Master. Always back up first and rebuild the BCD if the cloned drive refuses to boot.

For more clone mode and recovery guides, see Sector-by-Sector vs Intelligent Clone, Clone a Hard Drive with Bad Sectors, 4K Alignment When Cloning an SSD, and Clone an MBR Disk to a GPT SSD.

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