The film, directed by Hansal Mehta, stars Bajpayee as professor Shrinivas Ramchandra Siras, who was fired from his job because of his alleged sexual orientation.
"The biggest challenge was, to capture the loneliness in the man's eyes and portray that. That was difficult. To show loneliness in the body, on your face, that was most difficult thing to do," Manoj told reporters at the trailer launch of the film here.
'Aligarh', which is slated to release on February 26, also stars Rajkummar Rao, who plays a journalist.
Recently, filmmaker Karan Johar saw "Aligarh" and was all praise for the film.
Mehta says he is glad Karan "accepted" the movie.
"Karan saw the film and gave his reaction. I don't want to reiterate that... We used to always think we are outsiders in the film fraternity. On one hand there are those who make glittering, fantasy movies with big stars and on the other hand, we who make films where we try to uphold art and culture.
"The difference was in our minds. Yesterday when we showed the film to Karan, I met him for the first time in my career of 20 years. I felt I was wrong till now because he accepted the film," Mehta added.
Film editor Apurva Asrani, who has penned the movie, said he was unhappy with Karan for a long time because of the way he portrayed homosexuals in his home production 'Dostana'.
"Karan had made 'Dostana' and the way he depicted homosexuality I was very sad. It was shown that homosexuals can be only made fun of on screen. The trend has been going on.
"I had written articles against Karan (and) 'Dostana'. When we met two-three times we were not speaking with each other. But when Karan heard about the issue of 'Aligarh', that nobody has the right to ask about what you're doing in you're bedroom, he started understanding that (the film)," Asrani added.
Asrani further said he was happy that Karan thought "Aligarh" is a progressive film.
"I heard that Karan has accepted that may be he did stereotype (homosexuality) in 2008, which had some reasons.
But he has accepted this film as a progressive movie and that is why he has come out to support the film and now we are friends," he noted.