Hi,
    I tried various things and now I have another doubt.  When I am loading the
  private key generated of RSA algo type, am I supposed to use write binary file or
  any other way specifically for loading private key file into card is there.

You might want to look at Ssh.java and scard.c from OpenSSH for guidance.
The rsa private key is kept in a particular file, fid 0x0012.
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