but when I print, it prints the files that have a file size of zero as well (prints all the files).

Of course it does print all files, since you print the elements of @files, not @newfiles.

But then, the array @newfiles would contain zero length elements, since you add $file1 to the array in a convoluted way (see push), which at that point is undefined.

Adding

use strict;
use warnings;
[download]

to the top of this code snippet's scope would catch that (and force you to declare the variables you use). See strict, warnings