You can connect to your PS3 via FTP when you are running MultiMan. Download FileZilla and install it. Look at MultiMan to get your PS3's IP address and type that into the field at the top of FileZilla and click Quick Connect. Browse to the folder where you store game backups (usually \dev_hdd0\GAMES\) and find the games you want to delete.
They will be named by their ID and not their natural name (i.e. BLUS090506) so you will have to look up the id's of the games you want to delete. Be sure not to delete any other files or you will soft-brick your PS3 and be forced to reformat it. If deleting the files via FTP does not clear up the space, you may need to rebuild the HD database from the recovery menu. Enter the recovery menu by following these steps:
1. With the system in standby mode. Press and hold the power button down until the system turns on and then off again. Release the power button.
2. After about 1 - 2 seconds press and hold the power button again, until you hear 2 consecutive beeps. Release the power button. During this step you will actually hear three beeps. There will be one single beep then a short delay followed by 2 consecutive beeps. Only release the power button after you hear the 2 consecutive beeps.
At this point the PS3 Recovery Menu will be shown on the screen.
Select Rebuild Database from the menu.