Since you have the input lines as an array, easiest would be to use grep.

my @newlines = grep{/\S/}@lines;  #move only lines that have 
                                  #a non whitespace char to the left
or
@lines = grep{/\S/}@lines;
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Update:
Normally when reading text files, I read it line by line instead of creating an in memory array.

For input I normally allow any number of "unseeable" whitespace chars. A blank line often may have an extra space in it that you can't see, especially if the input file is something that a human might edit.

while (<FH>) # update: was: while (my $line = <FH>)
             # don't really need "my line" here
{
    next unless /\S/;  #skip blank lines
    next if /^\s*#/;   #skip comments, or whatever...
    blah, blah
}
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