We just had an external BSA audit in which three technical CTR problems were noted. Those include: failure to indicate BSA/Regulator Code (noted on one CTR), using a post office box instead of a street address for the bank in item 38 (noted on one CTR), and failure to indicate a date of signature on item 46 (again noted on one CTR).

The external auditor said we should consider filing amended CTRs. We are attempting to do just that, but when filing an amended CTR you are required to complete all of part III and only the item you changed in section I and II. Part III is the bank's information, while part I and II are the transaction specific sections. The amendments we need to make on these three CTRs are in part III. How do we need to do this or is filing amended reports in these situations not necessary? Suggestions please!

I have always done, and recommended, a copy of the original CTR be included with the amended one. In that manner it is clear what information was amended and what remains from the original filed version. [note: I have not done any e-filing, so I do not know what impact that would have]
I have also recommended banks amend due to corrections in Part III.

Just follow the instructions on the form - it is included under Item 1a.

Here are the instructions under Item 1a. Amends Prior Report. If this CTR is being filed because it amends a report filed previously, check Item 1a. Staple a copy of the original CTR to the amended one, complete Part III fully and only those other entries which are being amended.

So we need to mark box 1a, complete all of Part III and attach it to the originally filed CTR?