Filing taxes as "married but filing separately" will affect my immigration process?

Filing in the "married but filing separately" category should not stand in the way of success with an Application to Remove Conditions. Copies of 2012 and 2013 tax returns showing that each spouse was identified as married and living at the same address will be helpful, regardless of the "filing separately" detail, especially when accompanied by an appropriate range of other documents reflecting that the couple continues to live together in a bona fide marriage. It would be wise to work with an immigration attorney to assure proper preparation and full documentation of the application.
David N. Soloway
Frazier, Soloway & Kennedy, PC
Atlanta, Georgia

There is no requirement that you file jointly any more than there is for United States citizens. I have assisted clients with this type of issue and provide USCIS with documentation of the percentage of married couples who do not commingle their finances. It has not been a problem in the past and if the marriage otherwise satisfies USCIS that it is genuine, you should not have one either.

Apparently none of your parents had to ask for US immigration benefits.. Unless you have children together, it is always best, at least until you remove conditions and obtain US citizenship to file "married, filing jointly". Anything short of that could run the risk of CIS suspecting your marriage is one of convenience geared to procure green card benefits.

Filing married but separately is almost a certain guarantee of a BIG DELAY in removing the conditions.
You can avoid co-mingling, but still keep immigration happy by having 3 bank accounts:
1. His
2. Hers
3. Ours
It's not too late to talk to an attorney.

This is certain to contribute to the likelihood of a request for evidence or interview. You can overcome this with other evidence of the marriage but filing jointly is a huge plus.

It's better to file married joint, but it's not dispositive if you have a lot of other evidence. NEVER file as "single" or "head of household" which indicates you don't live together or are not married. They look at all of your joint documents as a whole, so one factor is not the end all be all, but each factor is weighed together. So these taxes will help you less than married joint taxes. Do you have lots of other "stuff" - ie bank statements jointly, credit cards, lease or mortgage, utility bills, insurance, etc.?

I believe you should be fine! Be sure you have all supporting documents with you when going to USCIS. Good luck