You could use a flag.

my $comment;
while ($line = <CMDTXTF>) {
   @fld = split /\|/,$line;
   $comment++, next if $fld[5] =~ /\/\*/;
   $comment--, next if $fld[5] =~ / \*\//;
   next if $comment;
   print "$fld[0] $fld[2] sequence=$fld[4] $fld[5]" if $line =~ /$rege
+xp/;
}
[download]