YA Sci-Fi book with heroine that can change physical appearance. Spoilers.

[Aishwarya]

Spoilers
Heroine was a child when a spy type government agency ( headed by someone called Major i think) took her from her drug addict mother. Heroine has power to change her appearance. They trained her and now she is going on her first assignment. She is in love with her male instructor (hero). There is a female instructor/senior too who is also in love with the hero and can read minds. Heroine later finds out these two were manipulating her and reading her thoughts.
Her father (who left her as a child...taking her brother with him) is working against the agency and has powers too (i forgot what). Heroine's best friend who also works for the agency is kidnapped by her father.
After finding out that the agency's enemy is actually her father, heroine goes on the run with a friend to find her mother and get more info.
In the end of the book she goes with her brother after finding out hero was manipulating her. Her brother then alters/erases her memories to make her more malleable. Book ends at this point. Its the first book in an ongoing series if i remember right.

[Lobstergirl, au gratin]

What genre is it? That needs to be in your header.

[Aishwarya]

Its Ya Sci-Fi as far as i know.