Another possibility is "The Arrival" (1996), directed by David Twohy, starring Charlie Sheen and Ron Silver. In this movie, an astrophysicist discovers that aliens have arrived on Earth and are attempting to change the planet's climate to suit their needs. The aliens are also able to control the minds of humans. There is a scene in the movie where the protagonist meets with an alien on a rooftop.

Another movie that could fit your description is "The Host" (2006), directed by Bong Joon-ho. In this movie, a mutant creature created by chemicals dumped into a river abducts a young girl and takes over her body. The girl's family then sets out to rescue her, but are hindered by the government's efforts to contain the creature. The movie includes a scene where the protagonist and the alien creature have a conversation on a rooftop.

I hope one of these movies is the one you're looking for! Let me know if there are any other details or clues you remember that could help narrow it down.