Ajish,
Following points has to be taken care at hardware design level:
> Physical Isolation of sensitive components from noisy components.
> Control over Impedence,reflection & termination on signal traces.
> The use of solid planes for power & ground.
> Routing of signals to avoid right angle corners and stub traces.
> Routng of differential pairs to achive length matching.
> maintain distance between parallel traces to avoid cross talk.
> power supply de-coupling using capacitors.