This is an issue with these particular apps. TDSSKiller provides no automation methods beyond starting a scan (nothing for completing it and removal,) which wouldn't be much of an issue however it employs tactics to prevent methods such as isolating the window handle and sending keystrokes to it. Not saying it's impossible or out of the question in the future...
d7 does do some unnecessary MBAM prompts that it did not used to - however due to overwhelming user feedback, more were added in to accommodate additional functionality. I'm still thinking of ways to whittle them down without p*ssing off ppl who wanted the options there in the first place.
MBAM free is automated as much as it can be legally according to their licensing terms. I could do more, but I won't.
MBAM Pro, however is a different story. If d7 detects MBAM Pro on the system, it will fully automate the update process and the scans, is as it is allowed by their license.
So in many cases, I am only automating up to the point that is legally allowed. Beyond that, there are technical challenges to some custom apps. e.g. TDSSKiller, Combofix (due to it's nature of constantly terminating other processes,) etc.
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Personally I arrange my custom apps so that all of the ones requiring input are either at the beginning or end of the routine depending on what page I'm on, so I take all of that in one chunk and the rest is truly auto.
I also now keep different profiles with a comprehensive routine, and one that isn't so much, but can be fully automated.
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Now in the case of maintenance, most everything there can be fully automated, and if you MUST run one or two that aren't, you can shove them down to the very last actions it performs.
That all being said, here are my thoughts on automating malware removal beyond what I already do -- if I could do it for you, I would, but I would NEVER use it myself. The potential for false positives is great, and additionally too many times have I had an anti-malware app destroy Windows by removing a legitimate component (infected or not) and trying to reboot, only to receive a blue screen or other issue. Had I actually examined the malware logs prior to clicking the remove button, in virtually every case I could have isolated the legit component and prepared a fix/replacement that didn't suddenly cripple Windows while I was on the toilet and confuse the snot outta me when I got back.
