On Wednesday night, the two European giants meet at Camp Nou with the last-16 tie currently locked at 1-1 after last month's first leg at Stamford Bridge.
Messi will return to the Barcelona squad after missing Saturday's win over Malaga due to the birth of his child, and Fabregas has said that - if selected - he will look to give the Argentine attacker an "uncomfortable" night.
The 30-year-old is quoted by The Mirror as saying: "If I am lucky enough to play, it's true that we are positioned in nearby areas of the pitch, stopping him will be difficult but I will try to do everything possible so that he feels uncomfortable and can't put together a perfect performance.
"I see him as a rival who wants to win, and I want the same thing. We are in different teams and each player wants what is best for their own club. Obviously, you always have respect for each other."
Fabregas has started in each of Chelsea's seven Champions League matches this season.