Defragmenting doesn't do anything about arrangement of your folders or icons, or deleting files. It organizes the file pieces to be contiguous so each file can be accessed with minimal seeking. Sometimes this includes improving the organization so related files are located near each other, but none of this messes with what you see on the desktop or the contents of your folders.
As for your mp3 files, they take space like everything else* and may be fragmented or in the way of another file that's being worked on. If you watched long enough and remembered all your file names, you would recognize each of the files shown during a defrag though smaller files go by in a flash.
Anyway, I wouldn't defrag while you're having temperature problems. I've learned the hard way that exercising a machine to fix it can take a borderline system down the tubes. Listen to the guys above about airflow. If you can, set it on a fan to help airflow and see if the problems persist. If that takes care of things then you're in for a cleaning. If heat isn't the problem it may be time for a reinstall or at least a parallel install. (the glorious fix for all distant mystery problems
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(*The exception is that very tiny files may be stored entirely in the MFT. A bunch of very tiny files may eat up allocated MFT space and cause a fragmented MFT zone. That's why it's good to use a defrag utility that can optimize MFT's and pagefiles as well as normal files. Products like PerfectDisk or Diskeeper completely skunk NT/XP's defrag (which is really just a crippled version of Diskeeper).)