Depends on what the letter is referring to:
1) IF you don't run a business where you sell stuff, then it's probably referring to paying sales/use tax for buying a lot of stuff online for personal use that you didn't pay those MN sales taxes for. States are attempting to crack down on these sales, with various rates of success, and most retailers do asses state sales taxes, even with Online purchases. There is a section during the MN state interview that takes care of that...but only if you actually fill it out. So if MN now has a way to track your purchases from out of state, perhaps they are dunning you for those now.
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Or..maybe it's this:
2) But if you run a business where you sell a lot of stuff, or sell a lot of stuff online, then those MN sales taxes that you are supposed to be collecting and remitting to MN, are reported and paid to MN entirely separately from the TTX software. Those forms and reports and payments are only done thru MN's separate filing&payment system. In that case you would need to read the following....and maybe get help from a local CPA:
www.revenue.state.mn.us/forms_and_instructions/sales_tax_booklet.pdfand
http://www.revenue.state.mn.us/businesses/sut/Pages/Filing_Due_Dates.aspxand
http://www.revenue.state.mn.us/businesses/Pages/Tax-Types.aspx
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*