I am separated from my husband for approximately three years haven't filed taxes with him in the last 3 years but I'm still technically married how do I file or what should I put my marital status und

You have to file married separately unless you have a qualifying child so you could file head of household. 

If you have been filing single for the past few years you have been filing wrong.  Your choices are married filing jointly or married filing separately.   You are not Single.  As stated if you have custody of the children then you can file as Head of Household.