No, it will quarantine the virus and then you can fix it from there. The program will have an option to fix it or you can research what to do with the file.
The software if good enough will know what to do - or it will tell you what the virus is so you can do it manually.
The reason they quarantine it is so it can't spread anymore, but it can still harm your computer if not removed. Usually if it can't be removed and it is quarantined, it's a virus that infected an important file..and needs to be manually removed.
Good luck and post again if you need more help...finish up the scan first though