First glance -

• add use strict; use warnings to your code then clean up the errors and warnings.
• don't use $a or $b as variable names - they are reserved for use by sort
• use the three parameter open
• where does $fcount in addtoHash get a value? Make it explicit by passing the value into the sub rather than relying on a global.
• Don't prototype PrintArray - especially after it's first use!
• you probably want chomp @testdataset; before @testdataset = grep { $_ ne '' } @testdataset;
• @testdataset = grep { $_ ne '' } @testdataset; is redundant when followed by @testdataset = grep /\S/, @testdataset;
• what does for ($mainfile) { achieve?
• You test if ($exist == 0), but $i can == 0 and therefore $exist can == 0 (in addtoHash)

You could describe the output you expect. Sometimes knowing what is expected of a piece of code helps understand it - sometimes it helps misunderstand it :)

Update: more items added