while (my $line = <FH>){

	$line =~ s/[^\\]#.*//;
	$line =~ s/^#.*//;
	$line =~ s/\\#/#/g;

	print "$line";
}

##</code><code>##

\#Not a comment
#Comment
\#Not a comment  #But this is a comment
arbitrary text   #Comment     
arbitrary text   \#Not a comment
arbitrary text   \#Not a comment  #But this is a comment
arbitrary text   #Comment         \#This is part of the comment 

##</code><code>##

#Not a comment

#Not a comment
arbitrary text
arbitrary text   #Not a comment
arbitrary text   #Not a comment  
arbitrary text