They tend to stand out, but for this tutorial I've highlighted the lines on the model.
The best way to do this is to use a hobby knife, but files work too. Files will leave a rougher surface, but they're safer for younger hobbyists.
Anytime you're working with knives, you need to be careful. All scraping should be done away from yourself. If the knife catches on the model, stop and resume - more force will cause the knife to jump and can get away from you. Read more about hobby safety.
You don't want to scrape with the knife blade completely vertical. This will cause the knife to skip, creating a rough surface. Always tilt it one way or another.
This isn't just for removing mold lines, it's a gentle way of scraping models. Anytime you want to smooth or level an area, this is the way to do it.
If you leave a rough area from filing, this is a safe way to smooth it out.
It's harder to scrape in small, tight areas. You're better off using the following method and cut the mold lines off.
However, because of the sharp edge, it's easier to slice parts from the model, shave off more (wider area) than just the mold line or even flatten curved surfaces. By applying too much pressure or using too much force, you'll dig in to the model or slice off parts you'd rather keep.
Here's an example of one of the times I do use the cutting method. I place the blade on one end of the line, then scoop it through the gap. It's tricky to scrape concave surfaces.
Sometimes you'll get small sticks coming out of your models, these would be injection points. You might have to fold them out, but after you can slice them right off. This is also how you can clean the connector bits off from plastic sprues.
In places like his ridged tube, you may also want to scrape (not cut) sideways across the mold line, rather than with it.