Well, I guess you could be facing one of two problems (or both!):
a) your lines are rough
b) your scanner isn’t very good.
If it’s a) we’re talking about, then the only thing I can tell you is to practice. Line quality really is one of those things that only comes with time. My drawing teacher would make me do these silly exercises in which I’d hold my pen weird or just wobble it up and down the paper, stuff like that. It felt a bit useless at the time, but I think it actually did help me control my pencil that much better.
I also draw with a pretty soft (2B) 0.5 mechanical pencil, fyi. My uni drawing teacher hated that I used it but I don’t give a fuuuuck.
If it’s b), I think there’s a couple of things you can do. First, scan your stuff in really high resolution. Way higher than you need. My scanner back at my parents’ house is pretty bad, so whenever I need to use I set it to scan at 1200 dpi. When you make it smaller, it will help diminish this roughness that comes with a low quality scanner.
Also, you may want to try and tinker with the scanner definitions, if it allows you to. Lowering the contrast may help prevent an overexposed scan that makes lighter lines disappear (you can then adjust it to you taste in Photoshop).
Just as a reference, here’s a side by side comparison: straight from the scanner on the left, and after adjusting in Photoshop (levels + black and white) on the right. I scanned this with an Epsom Perfection V300, which I’ve been using for 5-6 years.
As you can see, it’s not a huge difference - to be honest, the best thing you can do to make a smooth scan is drawing smooth lines from the get go.