I was physically present in the US (MD) for only 16 days in 2020(Jan1-16).In,2018 and 2019 I was there in US for more than 300 days.Do I file as Non resident tax status?

Possibly.  What visa do you have?  Standard deductions may be available under some treaties.

 

IRS Publication 519 states:

 

Substantial Presence Test 

 

You are a resident for tax purposes if you meet the substantial presence test for calendar year 2020. To meet this test, you must be physically present in the United States on at least:

• 1. 31 days during 2020; and
• 2. 183 days during the 3-year period that includes 2020, 2019, and 2018, counting:
• a. All the days you were present in 2020, and
• b. 1/3 of the days you were present in 2019, and
• c. 1/6 of the days you were present in 2018.

For nonresident tax returns, TurboTax refers customers to Sprintax.

I was on H visa. But was on US payroll till end of March 2020, after I couldn't travel back due to Covid issues.

 It depends. What H visa did you have? Was it the H1 Visa , the H1-B visa, or some other H visa?

 

It's H1B

Yes, since you were only physically present in the US for 16 days, you will need to file as a non-resident. You must have been here for at least 31 days in 2020 to file as a resident. There are no COVID exceptions to this rule. You may file your 1040 NR with sprint tax as they are a trusted affiliate.