Girls keep saying I'm scary

[robstar]

As mentioned, we would need to actually be around you to see what's what, but there are a few things you can do.

Right off, know that the difference between being "creepy" and "mysterious" is a very fine line. If a girl likes a creepy dude he's mysterious, but if she dislikes a mysterious dude he's creepy accept that you'll just sometimes be creepy, but work to overcome it.

Scary has to do with power. If you're very deliberate, or firm, or blunt that is in your face masculinity and powerful. powerful mannerisms are firm and stiff bodied, really intense gaze, a fast and strong hand shake, etc. The power is obvious.

Keep that strength, but soften the edges. Think smooth edged titanium, or a marble sculpture. Very strong, but pleasing to the eyes and not rough it abrasive.

When looking at someone, make your piercing stare lazier. let your eyes droop a bit as if you're a bit sleepy. Like a mob boss, or a fighter who just plain outskills his opponent and is bored. Deep resevoir of power when needed, but not in use currently.

Relax in all postures and positions. Even when things are hectic be relaxed. When your boss is crawling up your ass and he's so far up there it feels like he's about to discover a lost civilization, be chill and smooth and tell him you get to name the discovery.

I don't really like to admit it, but I'm a scary guy also. But it's not bad after you accept it and work with it. If I Focus on someone and get intense people get nervous fast. But those people that see that power come out will also compare to to your almost lazy and smooth exterior when you're not about to wreck someone. That's when you go from being scary to being powerful, as people know when you have to unleash hell it comes quickly.

After getting used to it it's a vibe you carry with you all of the time and even strangers fall in line with it usually.

Generally in my experience I find the guys that girls call "scary" are not too strong and masculine, rather they have awkward, nervous mannerisms things like holding eye contact too much or not enough, blinking too much or not enough, high levels of face and body tension, poor posture etc. I don't know if I've communicated what I mean effectively, but think some of the guys you'd see on beauty and the geek. I'm generalising and I'm not saying that's the case for OP, I'd need to see him to know, but the fact that he's described himself as skinny, wearing glasses and being intellectual I feel some of the above may apply here.
Taking improv and acting classes would be a good way to loosen and correct some of those things. In fact I'd recommend it to any guy who's had troubles with women throughout their lives I'm not sure why I haven't recommended it to Catman or Sarge. Aside from subliminals, acting and performing has been the thing that improved my relationships with women the most, and I'm not just talking about the status, even with girls who don't know I do that. I've never met an actor/performer that didn't do reasonably well with women unless they're butt ugly. It enhances charisma.
So yeah I guess I agree with you that relaxation and removing tension is key.