I have written about shrinking the virtual disk of an OS X Virtual Machine here but recently I needed to shrink a Linux virtual machine. The process is almost identical across all of VMware’s products you just have to find the vmware-vdiskmanager tool.

The process

In most operating systems removing the files from the disk merely alters file tables so the operating system sees the space as free on the disk. For vmware-vdiskmanager to work, the disk space actually needs to be free which we can accomplish using a processed called zeroing.

The steps below could take quite some time depending on the files being deleted, speed of the disks, and CPU of the virtual machine.

On the Virtual Machine:

dd if=/dev/zero of=/EMPTY bs=1M
rm -f /EMPTY

Now that we have successfully zeroed the data use vmware-vdiskmanager to shrink the virtual disk.

On the VM Host:

"/Applications/VMware Fusion.app/Contents/Library/vmware-vdiskmanager" \
 -k "/path/to/your/vm/disk.vmdk"

Articles:
Growing, thinning and shrinking virtual disks for VMware ESX and ESXi,
Shrinking the disk image of an os x vm