We really need more info, but another thought is to scope your hash so that it will be 'emptied' automatically when the block it is contained in goes out of scope. Something like:

use strict;
use Data::Dumper;

my @thing = qw(a c g i t);

for my $id (1..5) {
   my (%infilestore,$seq);

   $seq .= @thing[rand @thing] for 0..2;

   push @{$infilestore{$id}}, (split //, $seq);
   print Dumper \%infilestore;
}
[download]

But why empty the hash? Do you have duplicate keys? Please give us more info.

jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)