I have a villain in my story who is very one-dimensional. It's difficult for me to portray him as three-dimensional, with a good side, without justifying his actions. He's the main scientist at this lab that experiments on kids (I know it sounds like Maximum Ride it's different I promise) and so far he's just like, kind of satanic in that every bit of pain is something he enjoys, both inflicting mentally and physically. Help? He's shitty to his family (he experimented on his daughter, she's the main character).
With villains, history is everything. Usually, they have some mysterious past hidden from the protagonist which spawns the motivation for their actions. Step into the shoes of your villain for a few moments. What evil was done to him that caused him to do evil towards others? Is it revenge, or something bigger? Even if the villain can justify his actions in his own eyes, it already goes a long way into creating a more complex character because it opens the readers eyes into the way this villain thinks. I've had a lot of trouble giving equal character value to my villains as my protagonists, but with a little thought these antagonists can become quite alluring characters!
I think the best way to deal with this is to think like your character and like @joufflucharlie said consider their history and also, consider their mental state. Did something happen to them in the past that made them like this or were they just born like this? Another suggestion is to look at well-developed characters who have similar traits. They don't have to be exactly the same but you might be able to better execute some aspects of your character's personality if you have seen how it can be done. For example (and I'm not sure if you will understand this reference) Professor Stein, when he is being overtaken by the madness, is the first thing I thought of when you were describing your character, they aren't exactly alike but their mental states seem somewhat similar. Anyway, hope that helps.
When writing a villain you have to consider what is his/her motivation. Very few villains see themselves as evil (no one is really evil by choice) like the other answers, history is everything. For example, my villain was abused and humilliated his whole life and now that he has power and control over others, he doesn't want to be powerless ever again. So, he indirectly (directly sometimes) kills anyone that he considers a threat to that sense of power. Best of luck.
