quarantining the files takes them pretty much out of commission. it isolates the suspicious malware from affecting your pc. Basically if they are files you needed, and they get quarantined, then you'll find that something won't work, a program. I have never had anything quarantined that was a needed file but not saying it can't happen. Think of it like the recycle bin for your deleted items. The files are moved out of your main sections of your hard drive but kept in a temporary bin until you delete them completely. A "safety net" so-to-speak, in case you changed your mind. in the same way quarantined files are put in a "bin". They no longer will cause you trouble, and if no adverse effects from them being quarantined, you're safe to remove them.

Hope this helps.