I recently bought a flat from a builder in India. Who is responsible for handling the sale deed and registration process? Do I need to pay the builder extra for these services? And besides registration fees and stamp duty, are there any additional legal fees I need to pay directly to the builder?

The builder is responsible for handling the sale deed and registration process. You should not have to pay the builder extra for these services as they are included in the cost of the flat. Besides registration fees and stamp duty, you may need to pay other legal fees like advocate fees, but these should be clearly stated in the agreement and are not payable to the builder.