Is there any other way of handling this data...

Since all the "captureID" values are unique, and these are the values that you want to use for fetching information about a given entry, I guess the question is, "why use an array at all?" I think a HoH (or even a simple hash) would work just as well:

my %outputFiles;

sub setOutputFile
{
    my ($id,$path,$type) = @_;

# HoH method:
    $outputFiles{$id}{path} = $path;
    $outputFiles{$id}{type} = $type;

# or, simple hash method:
#   $outputFiles{$id} = join "=:=", $type, $path;
}

sub getOutputFiles
{
    my $id = shift;

# HoH method:
    my $type = $outputFiles{$id}{type};
    my $path = $outputFiles{$id}{path};

# or, simple hash method:
#   my ( $type, $path ) = split /=:=/, $outputFiles{$id};

# ... do something with $path and $type ...
}
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