when you perform an EMC test, they have to point-out the values and result of the test. is not just simply pass/fail test. havin the results you can have an ideea what kind of noise do you have, and locate the source of the noise. there is conducted, and radiated noise. you said that you have problems with conducted noise. simply adding more capacitors or increasing the inductances may not solve the problem. what is the noise spectrum ? think about the parasitics which you can eliminate without redesigning the board, such as drain to GND capacitance due to improper heatsinkin or flux leakage of the transfomer which doesn't have copper shield arround. keep in mind the resonace of the filter elemnets when you choose their values !!!