Hi, If I understand you correctly, it should be pretty simple.
Just to be safe, back up the database.
First go to Auto Import, and make sure the drive you don't want available to MC is not listed there. If it is, delete the path. Set up auto import so just the drives/folders that you want available to MC are specified.
Now, to get rid of the files.
Let's say the files you don't want are on Drive G. In MC Go to drive G in the tree under files and list just the files on that drive.
Select all of them, right click and select delete. If I remember correctly, you'll come up with three options. DO NOT choose the last option, option 3, which is to physically delete the files. I'm not sure what the difference between one and two is; to be really safe try option 1 first. If that works great, if not option 2 will. Just remember, unless you actually want to purge your disk of the music/video files do not use option 3. You just want them out of MC. That should do it.
-Chris