You need to undo the chdir since you are using paths relative to the original directory.

Here's a convenient way of doing that:

use File::chdir qw( $CWD );
use File::Slurp qw( read_dir );

my @dirs = grep -d, read_dir('.');
for (@dirs) {
    local $CWD = $_;
    system '/somepath/foo.exe';
}
[download]

Or since we know we're just going one level down,

use File::Slurp qw( read_dir );

my @dirs = grep -d, read_dir('.');
for (@dirs) {
    chdir $_ or die;
    system '/somepath/foo.exe';
    chdir '..' or die;
}
[download]

Another way is to make the paths absolute.

Update: Added alternative.