Yes. In the MT state interview when asked about military situations that apply you should select both the active duty military and the nonresident military spouse options. You will then be asked to verify/enter your active military pay and also verify your spouse meets the requirements in the Military Spouse Relief Act; you should answer "Yes" as applicable and her pay will be excluded as well and any taxes withheld would show as a refund.
You should start in the federal interview to be sure the military questions are triggered in the state interview. In the federal "My Info" section be sure you have indicated your military status, that you were stationed in MT on PCS orders, have selected NV as yours and your spouse's resident state on 31 Dec and indicated that neither of you lived in any other states. Also, in the "My Info" section scroll down to "Other state income" and answer "Yes" you earned income in another state and select "MT" from the dropdown list. This will generate the MT nonresident return.
Finally, in the "Wages & Income" section when you enter your military W2 information you will arrive at a page asking about "Uncommon Situations" be sure to select the "Active Military Pay" item from the list.
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