This post will show you how you can create a clone (a backup copy is probably more accurate language) of a running virtual machine hard disk using nothing but a Standalone ESXi host without vCenter or VCSA.
The problem you will run into if you tried to do this in a straight forward fashion is the hypervisor lock on the virtual disk file will prevent you from creating a copy or backup of the virtual hard disk (<VM_NAME>-flat.vmdk and its associated descriptor <VM_NAME>.vmdk) while the virtual machine is running.

The trick to work around this constraint is to create a snapshot of the running VM which releases the lock on the -flat.vmdk file and transfers the lock to the new snapshot disk file.
In my example, the snapshot data file is named win2025dc1-000001-sesparse.vmdk and the descriptor is win2025dc1-000001.vmdk.

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Click here for direct download links to VMware software versions 6.x - 9.x (it's legit)

VM Directory Prior to Snapshot:

-rw-r--r--    1 root     root      144.0K Sep  1 09:14 vmware.log
-rw-------    1 root     root       81.0M Sep  1 09:09 vmx-win2025dc1-7791058fa68278eaed9ef6a11d63a4500273a3b5-1.vswp
-rw-------    1 root     root       81.0M Aug 25 08:14 vmx-win2025dc1-7791058fa68278eaed9ef6a11d63a4500273a3b5-2.vswp
-rw-r--r--    1 root     root          52 Jul 25 02:57 win2025dc1-8bd91f60.hlog
-rw-------    1 root     root        2.0G Sep  1 09:09 win2025dc1-8bd91f60.vswp
-rw-------    1 root     root       90.0G Sep  1 09:14 win2025dc1-flat.vmdk
-rw-------    1 root     root      264.5K Sep  1 09:09 win2025dc1.nvram
-rw-------    1 root     root         505 Sep  1 09:09 win2025dc1.vmdk
-rw-r--r--    1 root     root           0 Jul 12 06:49 win2025dc1.vmsd
-rwxr-xr-x    1 root     root        3.7K Sep  1 09:09 win2025dc1.vmx
-rw-------    1 root     root           0 Sep  1 09:09 win2025dc1.vmx.lck
-rw-------    1 root     root        4.0K Aug 24 14:32 win2025dc1.vmxf
-rwxr-xr-x    1 root     root        3.6K Sep  1 09:09 win2025dc1.vmx~

VM Directory After Snapshot:

-rw-r--r--    1 root     root      156.9K Sep  1 09:17 vmware.log
-rw-------    1 root     root       81.0M Sep  1 09:09 vmx-win2025dc1-7791058fa68278eaed9ef6a11d63a4500273a3b5-1.vswp
-rw-------    1 root     root       81.0M Aug 25 08:14 vmx-win2025dc1-7791058fa68278eaed9ef6a11d63a4500273a3b5-2.vswp
-rw-------    1 root     root      366.0M Sep  1 09:17 win2025dc1-000001-sesparse.vmdk
-rw-------    1 root     root         317 Sep  1 09:17 win2025dc1-000001.vmdk
-rw-r--r--    1 root     root          52 Jul 25 02:57 win2025dc1-8bd91f60.hlog
-rw-------    1 root     root        2.0G Sep  1 09:09 win2025dc1-8bd91f60.vswp
-rw-------    1 root     root        2.0G Sep  1 09:17 win2025dc1-Snapshot1.vmem
-rw-------    1 root     root        3.5M Sep  1 09:17 win2025dc1-Snapshot1.vmsn
-rw-------    1 root     root       90.0G Sep  1 09:17 win2025dc1-flat.vmdk
-rw-------    1 root     root      264.5K Sep  1 09:09 win2025dc1.nvram
-rw-------    1 root     root         505 Sep  1 09:09 win2025dc1.vmdk
-rw-r--r--    1 root     root         393 Sep  1 09:17 win2025dc1.vmsd
-rwxr-xr-x    1 root     root        3.7K Sep  1 09:17 win2025dc1.vmx
-rw-------    1 root     root           0 Sep  1 09:09 win2025dc1.vmx.lck
-rw-------    1 root     root        4.0K Aug 24 14:32 win2025dc1.vmxf
-rwxr-xr-x    1 root     root        3.7K Sep  1 09:17 win2025dc1.vmx~

Depending on whether you're dealing with thin or thick provisioned virtual disks, you can either opt to do the -flat.vmdk copy with the ESXi Host Client Datastore Browser or the vmkfstools builtin utility for the most reliability and flexibility.

vmkfstools syntax:
vmkfstools -i <input virtual disk> <output virtual disk> -d <disk format>

[root@esxi70:/vmfs/vol/truncated/win2025dc1] vmkfstools -i /vmfs/volumes/5c7c8eb2-dfb3e413-3690-001fbc0f29c1/win2025dc1/win2025dc1.vmdk /vmfs/volumes/HDD8TBVMFS6-1/temp/win2025dc1.vmdk -d zeroedthick
Destination disk format: VMFS zeroedthick
Cloning disk '/vmfs/volumes/5c7c8eb2-dfb3e413-3690-001fbc0f29c1/win2025dc1/win2025dc1.vmdk'...
Clone: 100% done.

Once you've created the copy of the input virtual disk, you can either create a new virtual machine and attach the existing virtual disk, or you can copy the original virtual machine files (.vmx, .vmxf, .vmsd etc) to the new storage location where the output virtual disk resides.

If powering off the VM is possible for you at all, I would recommend going that route and either exporting the VM to OVF in the Host Client GUI, or using the vmkfstools utility.

This article is strictly aimed at people who don't have vCenter or VCSA and who don't/can't power off the VM during the virtual disk migration. I'm aware there are third party tools which can perform the same task with a fraction of the effort.

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VMware 9x (ESXi, vCenter, VCSA)
VMware 8x (ESXi, vCenter, VCSA)
VMware 7x (ESXi, vCenter, VCSA)
VMware 6x (ESXi, vCenter, VCSA)
VMware Omnissa Horizon
VMware Workstation
VMware Remote Console
VMware Tools

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VMKFSTOOLS Help Information Output

[root@esxi70:/] vmkfstools --help
OPTIONS FOR FILE SYSTEMS:
vmkfstools -C --createfs [vmfs5|vmfs6|vfat]
               -S --setfsname fsName
               -Y --unmapGranularity #[bBsSkKmMgGtT]
               -O --unmapPriority <none|low|medium|high>
           -Z --spanfs span-partition
           -G --growfs grown-partition
   deviceName
           -P --queryfs -h --humanreadable
           -T --upgradevmfs
   vmfsPath
           -y --reclaimBlocks vmfsPath [--reclaimBlocksUnit #blocks]

OPTIONS FOR VIRTUAL DISKS:

vmkfstools -c --createvirtualdisk #[bBsSkKmMgGtT]
               -d --diskformat [zeroedthick
                               |thin
                               |eagerzeroedthick
                               ]
               -a --adaptertype [deprecated]
               -W --objecttype [file|vsan|vvol|pmem|upit]
               --policyFile <fileName>
           -w --writezeros
           -j --inflatedisk
           -k --eagerzero
           -K --punchzero
           -U --deletevirtualdisk
           -E --renamevirtualdisk srcDisk
           -i --clonevirtualdisk srcDisk
               -d --diskformat [zeroedthick
                               |thin
                               |eagerzeroedthick
                               |rdm:<device>|rdmp:<device>
                               |2gbsparse]
               -W --object [file|vsan|vvol]
               --policyFile <fileName>
               -N --avoidnativeclone
           -X --extendvirtualdisk #[bBsSkKmMgGtT]
               [-d --diskformat eagerzeroedthick]
           -M --migratevirtualdisk
           -r --createrdm /vmfs/devices/disks/...
           --sectorSize [512n|4kn]
           -q --queryrdm
           -z --createrdmpassthru /vmfs/devices/disks/...
           -v --verbose #
           -g --geometry
           -x --fix [check|repair]
           -e --chainConsistent
           -Q --objecttype name/value pair
           --uniqueblocks childDisk
           --dry-run [-K]
   vmfsPath

OPTIONS FOR DEVICES: 
           -L --lock [reserve|release|lunreset|targetreset|busreset|readkeys|readresv|
                     |registerkey|clearallkeys
                     ] /vmfs/devices/disks/...
           -B --breaklock /vmfs/devices/disks/...

OPTIONS FOR VMFS MODULE: 
           --traceConfig [0|1]
           --dataTracing [0|1]
           --traceSize <x> (MB)
vmkfstools -H --help

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