Hi Kayathri,
At first , i recommend you create one simple project to have a try , if it is the same problem ,
please check the PE driver version on your PC , install the latest one .
If it still can not work ,please uninstalled the PEMicro Eclipse Plug-in from KDS, and re-installed it again .
PE Micro debugging issues with KDS and MKL03 microcontroller
If only the FSFK project can not work ,
What about the system frequency of your project ?
If too low , the P&E can't working well with low frequency, you can use J-link to instead to have a try .
Hope it helps
Alice