Depending on your algorithm, you could try taking advantage of my and scoping; something like this:

while($condition){
   my @array;
..
..
}
[download]

That will restrict @array's scope to the loop.

You can also use undef to undefine the array.

Hmm Just had the idea I could just loop the array and pop(). Is that the best way?

This depends on how the algorithm using the array is set up.