Thank you for your reply. I will be applying under FSW as to be eligible under CEC I should have worked for 2 years as a Temp. Foreign Worker.
You should try reading the information at the link provided to you. If you had, you would know that CEC requires 1 year of full-time skilled work experience.
But in fact, you don't chose the program - if your profile is accepted into the pool, you will get an invitation to apply to the program for which you are eligible. If you are determined to be eligible (based on your profile) for both CEC and FSW, you will be invited to apply for CEC.
Another thing is that I was getting my remuneration paid by my employer in Home country while I did my clinical fellowship in Canada. I am just curious to know how will IRCC interpret this? Can they refuse my application by saying that how can you be working full time in both the countries at the same time?
This is a bit trickier, but not impossible, many others have similar situations and have succeeded. You will need letters of employment from BOTH your home country employer (will need to include details on remuneration and benefits), and the Canadian "employer" (whoever supervised your fellowship) will have to focus on your job duties and responsibilties.
The only thing I would caution about is if the Fellowship was funded under a government program that requires you to return to your country, the experience might be excluded.
Also, can I also show my Clinical Fellowship as my educational qualification or just work experience?
From CIC's perspective, the only thing that "counts" as an educational qualification is a diploma or degree. (For an employer, on the other hand, on your CV, it would make sense to include it in both places). I suggest showing it as work experience only in your profile, because if you show it as "education" then you will run the risk of a VO thinking you were a student and excluding the experience.