virudinesh: ++ for your question this time. What you were looking for is the destroy function. I have added a few global variables for convenience. In both subs, I use the same variable for the new frame and destroy it first (if it was defined before). I hope this is close to what you wanted to achieve. I removed a bit of code just for clarity. Please always use strict; use warnings;

use strict;
use warnings;
use Tk;
my $mw = new MainWindow(-background=>'Gray');
$mw->geometry("1400x800");
$mw ->optionAdd('*background','Gray');
my @wb;
my $file;
my $flag;
my $frame_name;
my $frme_window;
my $def_path1;

$wb[0] = $mw->Radiobutton(
    -variable => \$file,
    -command  => \&toclink,
    -text     => 'TOC LINK',
    -font => "r18",
        -width       => 17,
        -foreground  => 'black',
    -value =>  1)->pack(-side=> 'top',-anchor=>'w',)->place(-relx =>0.
+0,-rely =>0.20);

$wb[1] = $mw->Radiobutton(
    -variable => \$file,
    -command  => \&chapterlink,
    -text     => 'CHAPTER LINK',
    -font => "r18",
        -width       => 17,
        -foreground  => 'black',
    -value => 2)->pack(-side=> 'top',-anchor=>'w',)->place(-relx =>0.0
+15,-rely =>0.25);

$wb[2] = $mw->Radiobutton(
    -variable => \$file,
    -command  => sub {$flag =3;},
    -text     => 'FIGURE LINK',
    -font => "r18",
        -width       => 17,
        -foreground  => 'black',
    -value    => 3)->pack(
    -side     => 'top',
    -anchor   => 'w',)->place(-relx =>0.007,
                                                            -rely =>0.
+30);

MainLoop();
sub toclink()
{
        $frme_window->destroy() if defined $frme_window;
        $frme_window = $mw -> Frame(
                -background => 'DarkGray',
                -relief => 'sunken')->pack(-ipadx => 330,-ipady =>0, -
+side => "right", -fill => "y");
        $frme_window->Label(
                -text =>"Do You Want Give Input Styles: ",
                -font => 'Verdana 10 bold',
                -foreground  => 'dark red',
                -background => 'DarkGray',
                -height => 1,-width =>28) -> pack( )->place( -relx =>0
+.02, -rely =>0.08);
        $frme_window->Button(
                -foreground  => 'dark red',
                -text => "yes",
                -font => 'Verdana 8 bold', 
                -height => 1,
                -width => 10,
                -background => 'DarkGray',
                -command => \&enable) -> pack ( )->place(-relx =>0.43,
+ -rely =>0.08);
        $frme_window->Button(
                -foreground  => 'dark red',
                -text => "No",
                -font => 'Verdana 8 bold', 
                -height => 1,
                -width => 10,
                -background => 'DarkGray',
                -command => \&disable) -> pack ( )->place( -relx =>0.5
+7,    -rely =>0.08);
}

sub chapterlink()
{
        $frme_window->destroy() if defined $frme_window;
        $frme_window = $mw -> Frame(
                -background => 'DarkGray',
                -relief => 'sunken')->pack(-ipadx => 330,-ipady =>0, -
+side => "right", -fill => "y");
        my $butn =$frme_window->Label(
                -text =>'CHAPTER LINK  ',
                -font => 'Verdana 15 bold',
                -foreground  => 'dark red', 
                -background => 'DarkGray',
                -height => 1,
                -width =>23) -> pack( )->place( -relx =>0.3, -rely =>0
+.1);
        my $labl = $frme_window->Label(
                -text =>"Chapter Files ",
                -font => 'Verdana 10 bold',
                -foreground  => 'dark red',
                -background => 'DarkGray',
                -height => 1,
                -width =>15) -> pack( )->place(-relx =>0.01,    -rely 
+=>0.30);
        my $path_text6 = $frme_window->Entry(
                -textvariable => \$def_path1,
                -font => 'Verdana 8 bold',
                -width => 35,
                -background =>'white')->pack(-expand => 1)->place(-rel
+x => 0.20, -rely => 0.3);
        my $path_butn1 = $frme_window->Button(
                -foreground  => 'dark red',
                -text => "Browse",
                -font => 'Verdana 8 bold', 
                -height => 1,-width => 10,
                -command => \&browsecl) -> pack ( )->place(    -relx =
+>0.65,    -rely =>0.3);
        my $path_buttn2 = $frme_window->Button(
                -foreground  => 'dark red',
                -text => "Submit",
                -font => 'Verdana 8 bold', 
                -height => 1,
                -width => 10,
                -command => \&submitcl) -> pack ( )->place(-relx =>0.8
+0,    -rely =>0.3);
}
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