Careful design and layout, filtering, shielding and a bit of luck.
Are you building/designing one ? As a general rule I would suggest it is better to buy one that has already been designed and is compliant...why re-invent the wheel (or SMPSU)?
Of course, designing and building one for fun is fine , but then it doesn't matter too much if you don't comply as it will just be an exercise.
Del
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health warning: These posts may contain traces of nut.
EMI and EMC are big design challenges in switch mode power supplies and DC to DC converters. You have to consider all of the stray capacitances and inductances in the circuit. It is one of the more challenging aspects of design. Good input and output filters will significantly reduce the conducted emissions of an existing design and good shielding will help with radiated. For a new design you can reduce the emissions by minimizing the coupling via stray capacitance and stray inductance. Strategically placed ground Shields can short circuit some of the excess switching noise also.
Their are several good books on the subject but for new supply designs experience is a big help.