use strict;
my $str = '\\usepackage{test}%COMMENT1
TEXT
%COMMENT2
TEXT
Value is 10\\%, this should not be removed. %COMMENT3
begin{tikz}[
important 1,
%COMMENT4
important 2, %COMMENT5
]
TEXT
%COMMENT 6
TEXT
Table: value1&value2\\\\%COMMENT7
Table: value1&value2\\\\ %COMMENT8
Table: value1&value2 \\\\%COMMENT 9
Table: value1&value2\\\\% COMMENT 10
Table: value1&value2\\\\\\\\%COMMENT11 ';
my $regex = qr/(?<!\\)(?:\\\\)*\K%.*/mp;
my $subst = '';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html