what about:

while(<>) {
 chomp;
   if(/^FT.*/) {
     $ft_flag ++;
     next;
    }
   if(/^FH.*/) {
     $fh_flag ++;
     next;
    }
 if($ft_flag) {...; next;}
 if($fh_flag) {...; next;}
 if(/^BH.*/) {
    $current_bh=$_;
    next;
  }
  if(^0006.*) {
    do_whatever_using($current_bh,$_);
    next;
   }
}
[download]

@lines = <>; #Slurp the whole thing.
$fh = shift @lines; #First line of whole is FH line
$ft = pop @lines; #Last line of while if FT line
chomp ($fh,$ft); #get rid of newlines
@segments = split /^BH/, join "",@lines; #split it up based on a BH at
+ beginning of line;
shift @segments; #First segment will be empty.
foreach $segment (@segments) { #loop through segments
    $segment = "BH".$segment; #replace missing BH at beginning that wa
+s removed by split
    @lines = split /\n/,$segment; #split the segment on new lines
    chomp @lines; #get rid of newlines
    $batchhead = shift @lines; #first row is the Batch header
    foreach $trans (@lines) { #Loop through remaining
        process($trans, $batchhead); #process individual lines
    }
}
[download]

$fh = <>; #first line of input is FT
chomp $fh; #get rid of newlines
$/ = "\nBH"; #set Input record seperator to newline followed by BH
while (<>) { #loop through each chunk
    @lines = split /\n/,$_; #split chunk into lines
    chomp @lines; #get rid of newlines;
    $bh = shift @lines; #BH is first line.
    $ft = pop @lines; #on last iteration FT will be last line, otherwi
+se the lastline is a bare BH
    ($bh =~ /^BH/) || ($bh .= "BH" . $bh");  #if $bh doesn't start wit
+h BH then put it back.
    foreach $trans (@lines) {
        process($trans, $bh); #each remaining line is a single transac
+tion line
    }
}
[download]

my $fh = new FileHandle($fileName,">");
if (! defined $fh) {
  print STDERR "Error reading $fileName\n";
  exit(2);
}
my ($bh,$fh,$ft);
while (my $line = <$fh>) {
  chomp($line);
  if ($line =~ /^BH/) {
    $bh = $line;
  } elsif ($line =~ /^(F[HT])/) {
    eval("\$" . lc($1) . " = $line");
    next;
  } elsif (defined $bh) {
    callSub($line,$bh);
  }
}
close($fh);
[download]