# open the input and output files

open( my $in_fh, '<' ...
open( my $out_fh, '>' ...

# operate on a single line at a time rather than reading the
# input file in all at once (more memory-efficient if the
# input file is very large)

while( my $line = <$in_fh> )
{
    # skip the line if it contains only white space,
    # otherwise print it to the output file

    next if $line =~ m/^\s*$/;
    print $out_fh $line;
}

close $in_fh;
close $out_fh;
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