Here is a very simple way to clear the MBR on computers using the Linux PXE. Boot the Linux and send this command in a shell script or manually from the console: (Just be sure to replace /dev/sd* with your proper device)
Clobber the MBR and partition table: dd if=/dev/zero of=/dev/sd* bs=512 count=1
Clobber the MBR leaving the partition table in tact: dd if=/dev/zero of=/dev/sd* bs=446 count=1
You can of course use the dd command to zero your entire drive if you have time and patience: dd if=/dev/zero of=/dev/sd*