I recently called the Correspondence Unit because we had a CTR that we thought may have been submitted twice. I called to see if they received one or two CTRs from us on that person. The person that helped me needed specific information because we file electronically, such as date of batch submission, amount, etc. and he was more than willing to assist me. I believe that calling them is worth a shot at least to confirm that they received the CTR you are looking for if it is only one or very few (it may be harder for them to locate if you mailed it in via snail mail though).
For confirmations on regular CTR submissions:
For CTRs that were mailed in, I am not aware of any confirmation provided by the IRS.
For CTRs submitted electronically, we receive a report that is automitacally generated by our core processor listing submitted CTRs that have been accepted by the IRS.
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"I shall permit no man to narrow and degrade my soul by making me hate him." ~ Booker T. Washington