I prefer Path::Class

use Path::Class qw( file );

print(
    file('A:\\B.CD(E)~!@#$%^&\\E\\F.txt')
        ->relative('A:\\B.CD(E)~!@#$%^&'),
    "\n"
);
[download]

You could also use File::Spec::Functions

use File::Spec::Functions qw( abs2rel );

print(
    abs2rel('A:\\B.CD(E)~!@#$%^&\\E\\F.txt',
        'A:\\B.CD(E)~!@#$%^&'),
    "\n"
);
[download]

Both of the above return E\F.txt because .\E\F.txt is redundant. You can prepend .\ to the result if you insist on its presence.