It isn't a safe thing to do but you could close the file after reading it into your array. Then re-open it for output open $fh, ">", "file.txt" or similar which will clobber (clear the contents) your file then write to it. The danger is that a minor mistake in your program could wipe out or mangle the original file. You could write to a test file until you finish debugging.

Yes, I made as you wrote: I closed the file and re-open with > property and all are working)) this is our last code

#!/usr/bin/perl -w
use strict;
use warnings;
use Cwd qw();

my $path = Cwd::cwd();
my $date = localtime();
my $count=0;
my $count_file = 0;

my $report = "$path/report_$date.txt";

open (FINDIT, "find $path -name '*.js' -type f -print |") || die "Coul
+dn't execute find!\n";

while (my $filename = <FINDIT>) {
    $count_file++;
    open (TABLETKA, "$filename") || die "Can't open $filename: $!\n";
    my @lines = <TABLETKA>;
    seek(TABLETKA,0,0);
    my @clean = <TABLETKA>;
    foreach (@lines) {
            if ($_ =~ m#(document\.write\('<iframe.*)(</iframe>'\);)#)
+ {
        foreach (@clean) {
            $count++;
            if ( s{([[:space:]];document\.write\('<iframe.*)(</iframe>
+'\);)}{ //eof} ) {
            close (TABLETKA);
            open (APP, ">$filename") || die "Can't open FOR WRITING $f
+ilename: $!\n";
            print APP @clean;
            close (APP);
            
            open (REPORT, ">>$report") || die "Can't open a report.txt
+: $!\n";
            chomp($filename);            
            print REPORT "$count_file. FILE: $filename\nINFECTED LINE 
+NUMBER: $count\nCLEANING DATE: $date\n\n";
            close (REPORT);    
            $count = 0;
            }
            elsif ( s{([^[:space:]])(;document\.write\('<iframe.*)(</i
+frame>'\);)}{$1; //eof} ) {
            close (TABLETKA);
            open (APP, ">$filename") || die "Can't open FOR WRITING $f
+ilename: $!\n";
            print APP @clean;
            close (APP);
            
            open (REPORT, ">>$report") || die "Can't open a report.txt
+: $!\n";
            chomp($filename);            
            print REPORT "$count_file. FILE: $filename\nINFECTED LINE 
+NUMBER: $count\nCLEANING DATE: $date\n\n";
            close (REPORT);
            $count = 0;
            }
            elsif ( s{(;document\.write\('<iframe.*)(</iframe>'\);)}{ 
+//eof} ) {
            close (TABLETKA);

            open (APP, ">$filename") || die "Can't open FOR WRITING $f
+ilename: $!\n";
            print APP @clean;
            close (APP);
            
            open (REPORT, ">>$report") || die "Can't open a report.txt
+: $!\n";
            chomp($filename);            
            print REPORT "$count_file. FILE: $filename\nINFECTED LINE 
+NUMBER: $count\nCLEANING DATE: $date\n\n";
            close (REPORT);
            $count = 0;
            }
            }
        }
    }
}
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Enough codes make shapes. (Hamidjon)