deleting files in itunes

Sorry, really basic question.  I have mostly used atv for video streaming from my pc (windows xp) so really haven't used my itunes a lot.  I want to clean my itunes library.  I've only had itunes since I've had atvflash so I don't know the basics so bear with me.  When cleaning the library on itunes, I know about finding duplicates and such and holding down shift (option) to find exact duplicates, but I'm not clear on deleting files.  Since my media mostly not itunes purchased but is cd backups etc, will deleting files on my itunes library delete them from my hard drive as well, or only from what itunes reads as being in the library. I'm not really sure if atvflash makes this any different or if you could see other media from non - itunes attained media so thats why I'm asking here.  sorry if its the wrong place.

Thanks

when you delete the file's library entry in iTunes you will be presented with an option to remove the associated file also.. if you take the option then the file is moved to trash, if not only the library entry is removed and the origianl file will remain it its location.

Thank you! : )