Yes, you want to use ImageMagick http://www.imagemagick.org/script/perl-magick.php
You can use it stand alone with its convert function as in:
convert mylogo.bmp mylogo.jpg
or in a script along the lines of:
#!/usr/local/bin/perl
use Image::Magick;
my($image, $x);
$image = Image::Magick->new;
$x = $image->Read('girl.png', 'logo.png', 'rose.png');
warn "$x" if "$x";
$x = $image->Crop(geometry=>'100x100+100+100');
warn "$x" if "$x";
$x = $image->Write('x.png');
warn "$x" if "$x";
Just save it in whatever format you want.