I am trying to implement a program for finding the remainder on division of 2 numbers n2/n1 such that
n1 is of the order of 2^32(having a few digits)
and n2 is the order of 2^65536(having about 20000 digits)

So far I have stored them in an array digit by digit.
How to find the remainder?
Could someone suggest any quick/fast /efficient algorithm or iplementation for the same.

It rather depends on what else is implement and how you have implemented your division.

For example if you have implemented the division as while number is greater than divisor subtract divisor from number then whatever is left when you finish is the remainder.

If you want a specific operator to get the remainder after division (% operator) I do not believe you can do this without doing the division or as part of the division algorithm. For integer arithmetic the remainder from dividing x by y (i.e. x/y) can be expressed as

x - ((x/y) * y)