Section 54F clearly stipulates that the property which you are going to invest to claim exemption u/s.54F, should be a property which is assessable under the head "Income from House property".No where it stipulates the Invested property should not be let out for commercial purpose. Such property may be let out or used for self occupation purpose. Just because you let out it for commercial purpose does not violate provisions of sec.54F. The deciding factor will be based on the following things
1) If you bought or construct a residential property and let out it for Bank to maintain its branch, such income you should offer it as Income from let out property under the head Income from House property. eligible for 54F
2) If you bought a Commercial property or construct shops in your building then not eligible for section 54F.
So whether eligible u/s.54F or not, consider the nature of registration of property you done with Municipality or concerned officials, Thank you.