Thanks Again. Works like I want it too! Seek was good idea. You're pretty brainy. Here's what I ended up using.

 #!/usr/bin/perl5.8.8

use strict;
use warnings;
#use autodie; dies if open/close...fail 

print "Enter file to process\t";
my $count = <>; #captures input from STNDIN and finds the file associa
+ted with that number
chomp $count;

tempProteinFamFileCreator(); #creates a temp file with protein family

sub tempProteinFamFileCreator
{
my $infile = $count."_ProFam"; #iterates through all the protein famil
+y files with the count variable
open (my $INFILE,"<", $infile);

my $flag = 0;
open (my $TEMPfa,">",'temp');

while(<$INFILE>)
{
        if ($_ =~/^##UniRef90_([\w\d]+) Protein Family/)
        {
        close ($TEMPfa);
        open ($TEMPfa,">",'temp');
        seek $TEMPfa, 0 ,0;
        }

        if ($_ =~/^>UniRef90_[\w\d]+\.UniRef100_[\w\d]+/ || $_ =~/^[\w
+\d]+/)
        {
        chomp $_;
        print $TEMPfa "$_\n"; 
        }

        if ($_ =~/^>File/)
        {
        close ($TEMPfa);
        }

} #end of while loop
close ($INFILE); #closes the $INFILE handle
} #end of subroutine tempProteinFamFileCreator
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