use strict;
use warnings;
use Data::Dumper;

my $arr = [
            [
              IMG0001 => [
                           {
                               y => 0,
                               filename => 'new value',
                               x => 0,
                           },
                           {
                               y => 0,
                               filename => 'cel.jpg',
                               x => 10,
                           },
                        ],
            ],
            [
                IMG0002 => [
                               {
                                  y => 0,
                                  filename => 'batman.jpg',
                                             x => 0
                              },
                              {
                                  y => 10,
                                  filename => 'robin.jpg',
                                   x => 10,
                             },
                          ],
            ]
         ];

   splice @{$arr->[1]->[1]}, 1, 1;
    print Dumper $arr;