I notice you're referencing a few undefined variables (@sample1 ...), if you add strict/warnings, they'll warn you about that and other things, and in the process cut your development time in half!

I'd like to help, but your problem description is too long and wordy for me :)

Please read How do I post a question effectively? and post short sample input, expected/wanted output, actual output, and explain how the actual output of your program doesn't match the expected/wanted output.

You might write something like this

#!/usr/bin/perl --
use strict;
use warnings;
use Data::Dumper;
#~ use LIMS::MT_Plate;
#~ use Microarray;
use autodie; # dies if open/close... fail

Main( @ARGV );
exit( 0 );


sub Main {
    if ( @_ == 3 ) {
        print BreakSomePlates(@_);
    } else {
        Demo();
        print Usage();
    }
} ## end sub Main


sub BreakSomePlates {
    my( $infile, $queryplate, $plateno, $query ) = @_;
    open my ($inFh),  '<', $infile; 
    while(my $line = <$inFh>){
        chomp $line;
        WalkThe( $line );
    }
#~     return "The sample $query placed in $queryplate is the location
+ $sample_name of Master Plate\n";
}

sub WalkThe { rand 666 }

sub Demo {
    my ( $Input, $WantedOutput )  = DemoData();
    my $Output = BreakSomePlates( $Input, qw' plate 1 b2 ');
    require Test::More;
    Test::More->import( qw' no_plan ' );
    Test::More::is( $Output , $$WantedOutput, ' BreakSomePlates works 
+as designed ' );
}

sub Usage {
    <<'__USAGE__';

NAME
    well_identifier.pl - extract well location ...

USAGE
    well_identifier.pl
    well_identifier.pl infile platename platenumber query
    well_identifier.pl infile Plate1/Plate2 b2
    ...

ARGUMENTS
    - infile 
        path to BAC's 384 tab delimited text file
    - Plate Number
        Plate1/Plate2,Plate3 or Plate4
    - Query 
        i.e. b2

__USAGE__

}


sub DemoData {

    my $Input = <<'__One__';
something
__One__


    my $ExpectedOutput = <<'__Two__';
blah blah
__Two__

    return \$Input, \$ExpectedOutput ;
}
__END__
not ok 1 -  BreakSomePlates works as designed
#   Failed test ' BreakSomePlates works as designed '
#   at pm.921846.pl line 40.
#          got: ''
#     expected: 'blah blah
# '

NAME
    well_identifier.pl - extract well location ...

USAGE
    well_identifier.pl
    well_identifier.pl infile platename platenumber query
    well_identifier.pl infile Plate1/Plate2 b2
    ...

ARGUMENTS
    - infile
        path to BAC's 384 tab delimited text file
    - Plate Number
        Plate1/Plate2,Plate3 or Plate4
    - Query
        i.e. b2

1..1
# Looks like you failed 1 test of 1.
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