Either the file you are reading doesn't contain the whitespace you think it does or you just can't see it when it prints. ;)

Perhaps you are printing extra newlines?

my @file = <DATA>;
foreach (@file) {
  print $_,".";
}
__DATA__
  2 spaces at the front and 2 spaces at the end
    one tab at the front and one tab at the end    
no spaces at the front or end but 5 spaces before the second     5
[download]

  2 spaces at the front and 2 spaces at the end
.    one tab at the front and one tab at the end    
.no spaces at the front or end but 5 spaces before the second     5
.
[download]

When printing try:

foreach $line (@file) {
  print $line."\n";
}
[download]

Alternatively, you could change Mr. Muskrat's code as follows:

my @file;
while (<$file>) {
  push(@file, "$_\n");
}
[download]