We could help you better if you gave us a small sample of your actual input data and the output you expect. As it is I have no idea what you are really asking for help with. Are you having trouble decoding a bunch of bits to determine what the instruction is? Are you having trouble simulating some form of processor? Are you having trouble opening a file and reading its contents? I simply have NO idea what your problem is.

Ok so this is part of what I have:

 byte 1               byte 2 (optional)
 bits      [ 7 6 5 4 3 2 1 0 ]  [ 7 6 5 4 3 2 1 0 ]
 opcode      - - -             
 mod               -           
 operand1            - - - -
 operand2                         - - - - - - - -
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And instructions:

 opcode | instruction | operands (mod 0) | operands (mod 1)
 -------+-------------+------------------+-----------------
 0x00   | jmp         | r1               | r2:r1
 0x01   | movr        | r1, r2           | rx,   imm 
 0x02   | movm        | r1, [ds:r2]      | [ds:r1], r2
 0x03   | add         | r1, r2           | r1,   imm

 flags
 
 cmp r1, r2 instruction results in:
    r1 == r2 => fl = 0
    r1 < r2  => fl = 0xff
    r1 > r2  => fl = 1
 
    jmpe r1
    => if (fl == 0) jmp r1
    else nop
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I am then given:

 0x00 0x00 0x00 0x01 0x03 0x02 0x03 0x02 0x03 0x02
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But pretty much like you said, I am in need of simulating a processor with given instructions.

So the key information you need is that you need to use the bit operators to manipulate the bits in each byte to extract the interesting bit fields. In particular use & (bitwise and) and a bit mask to isolate bit fields, and use the bitwise shift operators >> and << to move fields of bits about. For example, to isolate the op code you'd do something like:

use strict;
use warnings;

my $byte = 0b00100100;
my $opCode = ($byte & 0b11100000) >> 5;

printf "Opcode is 0x%02X\n", $opCode;
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Prints:

Opcode is 0x01
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See perlop for details about the various Perl operators.

True laziness is hard work