Hello @p_a_u_darshana ,
Yes, you have to flash first the bootloader on the S12 Board. You will find a dedicated chapter in the Motor_Control_Toolbox_Installation_Quick_Start Guide attached to our toolbox.
You can find the bootloaders location by typing the following command in Matlab:
winopen(fullfile(mbd_find_s12z_root, 'tools', 'BootLoader', 'RBF_Files'))
Hope this helps,
Marius