I have been using Atmega8 + POwer mosfets IRFP250 +Mosfet gate driver (Ti's UCC series)+48v PMDC motor (2HP Cont.)

Problem is

Without using any protection circuitary on the gate output of the PMW speed controller My atmega8 Mcu's internal oscillator gets burned up ,
So what should I opt to supress these spikes and reverse voltages...

 

Post a diagram of your circuit.

 

Block diagram

 

If you have a capacitor and diode across the motor as shown, then that should suppress the motor transient voltage so you may have a ground transient problem. Do you have a single point ground for the motor and processor? That is do you run the ground to a single point near the power supply, separately run from that point to the motor and separately to the processor? You don't want any of the motor ground current going through the processor ground.

 

How can I Isolate the Processor from motor ground,Because there is only a single power supply ,So how can I isolate the ground??

 

You can using two powers for uC and Motor, and you can also using photocouple to transfer the signal, it will isolated from two sides.

 

Sorry ,But 2 power supplies are not possibles because i am operation this thing from 2 12v series connected batteries.

 

Sorry ,But 2 power supplies are not possibles because i am operation this thing from 2 12v series connected batteries.

Then you should in series a photocouple with g of mosfet.