SPI interface with other board_AVR_ESK1100 or among Arduino itself

Every transfer sends one byte and receives one. You don't "clear the buffer". Sending something, and getting a response to what was just sent, involves at least two transfers. You can't get a response at the same time you are sending because each bit is transferred at the same time.

Perhaps read this:

I want to create a dummy IMU which will be Arduino board or EVK1100(which will act as Master and will send command for data) and other slave board will be Arduino board which will receive command from IMU master board(Arduino or EVK1100) and then send back required data on SPI bus.

I really don't understand what you are doing. Normally SPI is two-way. You don't flip backwards and forwards from slave to master just to get something back. Please read the link above carefully. Then ask specific questions.