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.

In reply to Re^2: trouble with a simple script by ikegami
in thread problem running executable in subdirectories by apollo

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