$ ls -1 *SNPtable*
2836_SNPtable_CLC_stringent.txt
2838_SNPtable_CLC_stringent.txt
2840_SNPtable_CLC_stringent.txt
5039_SNPtable_CLC_stringent.txt
$ cat script.pl
use warnings;
use strict;

@ARGV >= 1 or die qq[Usage: perl $0 file1 [file2] [file3] ...\n];

my $suffix_word = qq[Sample];
my $suffix_letter = qq[A];

my $argc = @ARGV;
my @header_in = split /\s+/, scalar <>;

my $header_out = "@header_in[0..2]" . qq[ ];
for ( 1 .. $argc ) {
        $header_out .= join( qq[ ], map { $_ . qq[.] . $suffix_word . $suffix_letter } @header_in[3..$#header_in] ) . qq[ ];
        ++$suffix_letter;
}

printf "%s\n", $header_out;

while ( <> ) {
        next if $. == 1;
        print;
} continue {
        close ARGV if eof;
}
$ perl script.pl
Usage: perl script.pl file1 [file2] [file3] ...
$ perl script.pl 2836_SNPtable_CLC_stringent.txt 2838_SNPtable_CLC_stringent.txt 2840_SNPtable_CLC_stringent.txt  5039_SNPtable_CLC_stringent.txt 
chromo pos ref alleles.SampleA refAllele.SampleA refCount.SampleA refFreq.SampleA altAllele.SampleA altCount.SampleA altFreq.SampleA alleles.SampleB refAllele.SampleB refCount.SampleB refFreq.SampleB altAllele.SampleB altCount.SampleB altFreq.SampleB alleles.SampleC refAllele.SampleC refCount.SampleC refFreq.SampleC altAllele.SampleC altCount.SampleC altFreq.SampleC alleles.SampleD refAllele.SampleD refCount.SampleD refFreq.SampleD altAllele.SampleD altCount.SampleD altFreq.SampleD 
chr1 30146 A A A 31 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55223 C C C 2 100 NA 0 NA
chr1 55987 C C C 19 100 NA 0 NA
chr1 62138 T T T 114 100 NA 0 NA
chr1 62233 A A A 110 100 NA 0 NA
chr1 64310 A A A 64 100 NA 0 NA
chr1 64321 A A A 17 100 NA 0 NA
chr1 64377 A A A 56 98 NA 1 NA
chr1 30146 A A A 10 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55987 C C C 8 100 NA 0 NA
chr1 62138 T C 0 0 C 10 100
chr1 62233 A A A 34 100 NA 0 NA
chr1 64310 A A A 37 100 NA 0 NA
chr1 64321 A A A 9 100 NA 0 NA
chr1 64377 A A A 27 100 NA 0 NA
chr1 65570 A C 0 0 C 2 100
chr1 30146 A A A 54 100 NA 0 NA
chr1 55217 G A/G 0 0 A 5 55
chr1 55223 C T/C 0 0 T 4 57
chr1 55987 C C C 17 100 NA 0 NA
chr1 56065 T T T 18 90 NA 2 NA
chr1 62138 T T/C T 19 70 C 8 29
chr1 62233 A G/A 0 0 G 16 66
chr1 64310 A A A 28 100 NA 0 NA
chr1 64321 A C 0 0 C 4 100
chr1 30146 A A A 23 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55223 C C C 2 100 NA 0 NA
chr1 55987 C C C 19 100 NA 0 NA
chr1 62138 T C 0 0 C 38 100
chr1 62233 A A A 108 100 NA 0 NA
chr1 64377 A A A 2 100 NA 0 NA
chr1 65570 A A A 3 100 NA 0 NA
chr1 66577 T T T 45 100 NA 0 NA