I would like to make a letter to the officer in charge of BIR but i don't know how to start with my letter with regards to our failure to comply with their requirements and I can't afford the penalty amount being charge for us. Please help me find the appropriate letter to make so as not to offend the person.
By "BIR" do you mean the Bureau of Internal Revenue?
Have you consulted an attorney? Depending on how much money you owe, it might be best to consult a professional before writing to the BIR.
If you do write, and you are admitting that you owe the amount they say, you could state that your current financial situation makes it impossible to pay the amount they are demading, and that you would like to make arrangements for some sort of payment plan if at all possible.