if I want column 1 entries to go in one array , second column entry to another and so on . How can i define my array

The easiest solution is to have an array or arrays, AoA for short. These are 2D arrays. See:

• perldsc - Perl Data Structures Cookbook - ARRAYS OF ARRAYS

To understand AoA's you'll need to learn about references:

• perlreftut - Mark's very short tutorial about references this explains 90% of what you need to know about references. Absolutely essential reading!!
• perlref - Perl references and nested data structures this explains the rest. You can skip this until much later in your Perl coding!

You can then store each field in $AoA[row number][column number]
It's unlikely you'll need to ask the user how many columns there are.

Update: doh! Cross posted with marto and hippo, though luckily I think together our posts explain different levels and aspects of the solution.

Text::CSV is definitely the way to go!