Q. Is the Bajaj CT 100 comfortable for daily commute of approx 100km nonstop riding upto 40-50 kmph?

I understand 50km up and 50km down, totals your 100km. For this kind of distance you will find that less travel time is better. So 150cc or more bike should be preferred. But as you are okay with lesser speed and travel time is not an issue, CT will save you money on fuel and is fairly comfortable to drive for 50km one way, considering your age is less than 50 years. It will help if you get a cushioned seat for a smooth travel experience ;-)

Yes if you can do it bike can It will take 2:30 hrs to do so

Great go on