These pushed values in a set of 4, can be any no of times in the last place of each input line.

But in your "Desired output" block there's only one set of four on a line? Then there's a line break, and the next line contains the continuation? Is that really what you want, or do you want the elements at index 7 in each array ref on one line? Then, you have those coordinate blocks neatly left-aligned at column 34. Is that a requirement? I'll assume it is.

At line 65, put brackets around @tmp, otherwise you will have a flat list in @finalarr.

From line 11 on things are getting messy. No need to dereference $cordinate_r into @refer, so no need for line 13.

To get at the data:

foreach my $ref(@$cordinate_r)
{
        my $line  = join ' ', @$ref[0..6];

        # splice field 7 into groups of four
        my @ary = @{$ref->[7]};
        my @coord; 
        while(@ary) {
            push @coord, join ' ', splice @ary, 0, 4 ;
        }
        
        no warnings 'uninitialized';

        # see 'perldoc perlform' for what follows

        write;
format STDOUT =
@<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @<<<<<<<<<<<<<<<<<<<<<<<<
$line, shift @coord
                                ~@<<<<<<<<<<<<<<<<<<<<<<<<
shift @coord
.

}
[download]

Output:

G6081 yaaX 5234 5530 + 6 6       244 480 540 480
EG10011 yaaA 5683 6459 - 6 7     693 480 1010 480
                                 10 560 469 560
EG11555 yaaJ 6529 7959 - 7 8     539 560 1010 560
                                 10 640 969 640
[download]

Be consistent with the alignment of your curlies!

There's more to 'go all perlmonks on you', no time now... look for an update of this node.

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}