I have got 2 files which I need to parse based on certain features but the files are too big as much as 3 GB so I am unable to use array or even storage variables.

So if the file is too big for one approach, you need to use another approach. I don't see what the problem is.

Reading some file into memory is all well and good if you have enough memory, but if it doesn't fit in memory, that's not the end of the known constellations of solutions. Obviously, you have to do some sort of paging to disk, either yourself or using a database. Just go from there.

Don't let one obstacle stop you from making progress on your problem, what ever it is. Try lots of different approaches, and remember Edison's attitude when someone asked him on his progress to find a suitable material for the filament of an electric light bulb. He didn't say he'd failed 400 times, he said he'd tried 400 different possibilities and hadn't yet found the correct one.

Onward!