I'm downloading visual studio 2010 professional through MSDN Academic Alliance. And I get the download is finished confirmation even before the progress of the download doesn't reach 100%. I extracted the iso file and it didn't have any problems or errors extracting its contents. But I noticed some sub folders are empty. Is it possible that I haven't really downloaded the full content of the archive?
Yes, it is very possible with many archive formats to have missing data when extracting an incomplete download.
What archive format is the download you're using in?