Eddy current can generate a secondary magnetic field. Any ideas on how to ignore the secondary magnetic field generated by eddy current? Any solutions which could be done by software?
Whatever you do in software will not change the reality. Thus I do not understand your question correctly. However, there at least two ways of fighting eddy currents in real use:
One is to make the magnetic elements composed of separate, insulated parts - like in power transformers or some electric engines. The other way is to use very poor electric conductors for magnetic elements - many ferrites fall in this class. If your software takes into account the electric conductivity - you're easily done.
According to Lenz law, it is necessary to produce extra inverse current source as a source of inverse Eddy currents. For EMI systems, check pls: http://anibal.gyte.edu.tr/dosya/102/~saksoy/Metal%20Detectors/Advanced%20Metal%20Detectors%20-%20Book.html