Assuming $var1, $var2, and $var3 are all different, then this:

if(($count != $var1) || ($count !=$var2) || ($count !=$var3))
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will always be true.

Your call to system("chosespectraldata.pl $spectralfile $var1 $var2 $var3 > $diroutput$output"); can also be replaced with:

my $cmd = 
  q#perl -F, -aane 'chomp @F; print join ",\t", @F[ grep(! /^(#
   . "$var1|$var2|$var3"
   . q!)$/, 0..$#F)] ' !
   . " $spectralfile > $diroutput$output ";
warn $cmd;
system( $cmd );
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see perlrun for details. also try this static cmd on your spectralfile:

perl -F, -lane 'chomp @F; print join ",\t", @F[ grep(! /^(1|10|6)$/, 0
+..$#F)] ' blah.txt
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