foreach my $Index ( 0 .. 10 ) {	
		
`Script Input:File_1[$Index], Paramater, Output: 'Results_File_1_'.$Index`;

@Results_1 = Parse the 'Results_File_1_'.$Index using subroutine and append to @Results_1;
		
`Script Input:File_2[$Index], Paramater, Output: 'Results_File_2_'.$Index`;

@Results_2 = Parse the 'Results_File_2_'.$Index using subroutine and append to @Results_2;
		
}
	
Do something with @Results_1, @Results_2 (both have to finished).