I ran your code, and saw one problem immediately.

#Here are some fake buttons using sub-canvas:
my $scan1 = $rightframe-> Canvas(-width => 64, -height => 54, -highlig
+htthickness => 0);
my $scan2 = $rightframe-> Canvas(-width => 64, -height => 54, -highlig
+htthickness => 0);
my $scan3 = $rightframe-> Canvas(-width => 64, -height => 54, -highlig
+htthickness => 0);

&scan1start;

MainLoop;

sub reset {
        my @buttons = ($scan1,$scan2,$scan3);
        foreach (@buttons) { $_-> destroy; }
        #&scan1start;
}

sub scan1start {
        if ($numscan1 == 0) {
                $scan1-> form(-left => '187', -top => '319');
                $scan1-> configure(-background => 'black');
                $scan1-> Tk::bind('<Button-1>' => sub {
.... etc 
.... etc
.... etc
}
[download]

You define $scan1, $scan2, $scan3 globally, then destroy them in your reset sub. Then without recreating them, you try to access them in &scan1start.

Although it dosn't address all your issues, you might start by tring something like this:

#!/usr/bin/perl
use warnings;
use Tk;
use strict;

my $mw = new MainWindow;
$mw-> geometry('640x480');
$mw-> resizable( 0, 0 );

my $numscan1 = 0;
my $numscan2 = 0;
my $numscan3 = 0;

my $leftframe = $mw-> Frame();
$leftframe->form(-left => '%0', -right => '%25', -bottom => '%99', -to
+p => '%1');
my $resetb = $leftframe-> Button(-text => 'Reset', -command => \&reset
+ )->form(-left => '%50', -top => '%50');

my $rightframe = $mw-> Frame(-relief => 'groove', -borderwidth => 1);
$rightframe-> form(-left => $leftframe, -right => '%99', -bottom => '%
+99', -top => '%1');

my $maincanvas = $rightframe-> Canvas(-background => 'blue', -highligh
+tthickness => 0);
$maincanvas-> form(-left => '%1', -right => '%99', -bottom => '%99', -
+top => '%1');

#Here are some fake buttons using sub-canvas:
#my $scan1 = $rightframe-> Canvas(-width => 64, -height => 54, -highli
+ghtthickness => 0);
#my $scan2 = $rightframe-> Canvas(-width => 64, -height => 54, -highli
+ghtthickness => 0);
#my $scan3 = $rightframe-> Canvas(-width => 64, -height => 54, -highli
+ghtthickness => 0);

my $scan1;
my $scan2;
my $scan3;

&scan1start;

MainLoop;

sub reset {
    my @buttons = ($scan1,$scan2,$scan3);
    foreach (@buttons) { $_-> destroy; }
    &scan1start;
}

sub scan1start {

 $scan1 = $rightframe-> Canvas(-width => 64, -height => 54, -highlight
+thickness => 0);
 $scan2 = $rightframe-> Canvas(-width => 64, -height => 54, -highlight
+thickness => 0);
 $scan3 = $rightframe-> Canvas(-width => 64, -height => 54, -highlight
+thickness => 0);

    
    if ($numscan1 == 0) {
        $scan1-> form(-left => '187', -top => '319');
        $scan1-> configure(-background => 'black');
        $scan1-> Tk::bind('<Button-1>' => sub {
            $numscan1 = 1;
            &scan2start; &scan3start; &scan1start;
        } );
        $scan1-> Tk::bind('<Button-3>' => sub { });
    }
    elsif ($numscan1 == 1) {
        $scan1-> form(-left => '187', -top => '319');
        $scan1-> configure(-background => 'white');
        $scan1-> Tk::bind('<Button-3>' => sub {
            if (($numscan2 == 0) && ($numscan3 == 0)) {
                $scan2->formForget;
                $scan3->formForget;
                $numscan1 = 0;
                &scan1start;
            } 
        } );
        $scan1-> Tk::bind('<Button-1>' => sub { });
    }
}

sub scan2start {
    if ($numscan2 == 0) {
        $scan2-> form(-left => '102', -top => '211');
        $scan2-> configure(-background => 'black');
        $scan2-> Tk::bind('<Button-1>' => sub {
            $numscan2 = 1;
            &scan2start;
        } );
        $scan2-> Tk::bind('<Button-3>' => sub { });
    }
    elsif ($numscan2 == 1) {
        $scan2-> form(-left => '102', -top => '211');
        $scan2-> configure(-background => 'white');
        $scan2-> Tk::bind('<Button-3>' => sub {
            $numscan2 = 0;
            &scan2start;
        } );
        $scan2-> Tk::bind('<Button-1>' => sub { });
    }
}

sub scan3start {
    if ($numscan3 == 0) {
        $scan3-> form(-left => '202', -top => '211');
        $scan3-> configure(-background => 'black');
        $scan3-> Tk::bind('<Button-1>' => sub {
            $numscan3 = 1;
            &scan3start;
        } );
        $scan3-> Tk::bind('<Button-3>' => sub { });
    }
    elsif ($numscan3 == 1) {
        $scan3-> form(-left => '202', -top => '211');
        $scan3-> configure(-background => 'white');
        $scan3-> Tk::bind('<Button-3>' => sub {
            $numscan3 = 0;
            &scan3start;
        } );
        $scan3-> Tk::bind('<Button-1>' => sub { });
    }
}
[download]

P. S. I also notice that you have recursive subroutine called in scan1start(). The way I set it up in the example, or in any Tk script, a recursive widget-creating sub is bound to cause havoc. By the way, why are you not using the createWindow method to embed those sub canvases?

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