Using the answering machine template as your basis (obviously, you need to change the recording so that each file is named uniquely, here is what you need to do:
1) In your main application, use a "Run TAP" step at the point you want to collect a voicemail message, and run the voicemail/answering machine TAP you are using.
2) In the voicemail application, make sure your global event labels (CALLER_GONE and APPLICATION_ERROR in the flowchart "Main") both go to the FINISH step in the "Main" flowchart. Also, when the last flowchart (Answeringmachine in the template application) exits, it must go to the FINISH step as well.
3) After the "Run TAP" step in your main application, add a "Compare" step, and check if @HOOK_STATUS = OFF-HOOK. If it is, the caller is still on the line, and you can decide where to route the caller. If not, the caller and/or the system has hung up the phone, so you should use a "Hang Up" step, and make sure the step is set to "Hang up and goto GLOBAL HANGUP label".
That should do the trick.
If, after you do all that, there are still problems you can't solve, please attach a log (the last post mentioned a log, but it wasn't present), and describe what is wrong.
On some of the specific points / questions you had:
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Is there a way to complete the answer TAP and return to the Finish in the IVR TAP?
Yes, this is essentially what I have described above.
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Do I have too many subdirectories
Not sure what you mean by this, but creating directories doesn't fail because there are too many (well, perhaps it could, I'm just not aware of a limit like this as I haven't yet encountered it). However, if you are trying to force one "Create Folder" step to create a directory, and multiple subdirectories to it all at once, this doesn't work. (I.e. You have to create each directory that doesn't exist one at a time.) If that is what you are trying to do, create multiple directories in a full directory path with one step, this is a problem.
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Does this qualify for help?
I'm not sure I understand what you meant with this question...