I'm using PSoC 3 family CY8C3866AXI-040 controller.
Again i have a doubt that for generating 1 msec or more,shall i go for timer or PWM.Please suggest me
You can either use PWM or Timer to generate 1ms Interrupt. The picture below shows how to do it using PWM. Configure PWM for a Period of 99. Connect an input Clock and configure it to give a fequency of 100 Khz. The terminal count output goes high after 1ms. Connect an ISR from system resources and configure the ISR to be triggered on rising edge.