my $hitname1;
my $hitname2;
while ( my $hit = $result->next_hit ) {
$hitname1      = $hit->name();
print ">" . $hitname1;
}

$result->rewind; # setzt den iterator wieder zurück.

while ( my $hit = $result->next_hit ) {
$hitname2      = $hit->name();
 while ( my $hsp = $hit->next_hsp ) {
print ">" . $hitname2 ;
 ..
 }
}