Re: How do I clean up an OS X VM?

This might initially increase the size of your VMDK, but you can make it smaller eventually.

1. In the Virtual Machine: "sudo pmset hibernatemode 0; sudo rm -f /var/vm/sleepimage"
2. Defragment the "Macintosh HD" partition inside your VM. There are tools for that such as iDefrag. If you don't want an extra license for your VM, convert your virtual disk to monolithicFlat (Preallocate enabled and without the split), temporarily rename your "-flat.vmdk" to "-flat.dmg", mount it in the host system and Defragment it from the host system.
3. Eject the DMG file and rename it back to vmdk. In VMWare Fusion, disable preallocation of the disk space and add back the "split into 2GB files"

You can also for Fusion 6, which might be of more help with the AHCI controller, but I haven't checked since I always preallocate my virtual machines (for performance reasons).