So 4 things I would say.
1 use a scanner, usually at 300 to 600 dpi if you want high to very high detail accuracy (mostly 600 if you are going to do some photo editing). I very strongly recommend playing with the settings, for brightness and contrast. I do not use my printer's scanning program. Instead, I just use regular old ms Paint, which is able to scan from the printer. I usually find that the best results is to lower the brightness and then increase the contrast, to try to make the paper turn pure white, the pensile dark but still detailed. The issue is that smudges will be exaggerated.
If you do not have a scanner, I recommend that when you take a picture, have the light come from the side, try to have something that is physically large or long, like, having the paper on a clipboard, and hold it up near a fluorescent kitchen lamp. A Fluorescent in the 4200 to 5400-kelvin range should do a pretty good job of being white, and the large (longe) area of the light means that the light will be very diffused, so that the image will be evenly lit despite things that could produce shadows, like that of the camera (which is also why the light should be to the side). The computer will she shadows and smudges and deliberate details and are not hard to remove without directly painting said effects out.
2 get a better monitor. If you are taking work from real life to your screen, You Must Get A Color Accurate Monitor. A cheap $150 usd TN type panel is absolute garbage, but what most people have (same with laptops). Colors are a bit yellow, tends to bake images look brighter or darker, and tends not to evenly represent brightness as colors will bleach out at the higher spectrum. If you need I can help you with picking a monitor for your budget, I use to help design custom pc builds all the time a few years back. You can see how good or bad your monitor is by trying to calibrate it manually using this
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, but you'll see you will not be able to make each test perfect. It is likely that when you currently work on things, what your screen shows you does not accurately reflect what the computer thinks the images looks like, so if you try to fix the image to look white on a slightly yellow screen, your image would actually be a bit blue, and noticeable on other screens that are not as yellow as yours.
3 Use Gimp. Gimp is like photoshop. it is #2 on the chart, but it is free, and if you are more familiar with photoshop but don't have it, there is a gimpshop version that recreates the photoshop feel and experience to make it more friendly to previous photoshop users. The main thing with gimp is to continue to edit and make improvements to your artwork. it can do way more than just brightness and contrast correction. I find that the level curve (I think in the new version 2.10.12 it is called the color curve tool or just curves) is one of the most important steps to get the right look and feel of a pencil drawing. Now for color, that is a bit more tricky, you can do hue-saturation correction and hope for the best, try tricks like making multiple layer duplicates and having them multiply or soft light the lower layers to better exaggerate the colors, but I find trying to color paper does not work due to it naturally wanting to be white, which tends to blow out the image. I would say play with coloring after the fact. You can try taking an picture of your drawing, get is as black and white as possible, and either turning color to alpha (transparent) to remove the white so you just have lines, and coloring underneath it, or keep the white, but have it set to multiply the colors of the layer below it, and paint on another layer under it, this way you can make color corrections without ever disturbing the drawn lines. While Gimp has the best layering and color mixing system, it sometimes is not the best drawing program, if you want to keep the feeling of being hand made and not digital, try using programs like Paint Tool SAI (I do not understand why some many other artist love this tool so much, it seems like a weaker version of gimp) or even more powerful, KRITA which has lots of tools and brush options and I wish I used it more. It also has a really good layering system, but I think it has the best brush options of any program, beating out photoshop, and other professional grade tools. And still free
I also recommend looking for plug in for gimp that involve having lots of effects, such as
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, which tends to be very useful for playing with ideas or possibilities.
4 If however, you want to really clean things up and have a clean look, the first step would be to make sure that you do clean artwork. What I have done is: sketch, scan, edit in gimp to be really faint, print, and make a clean sketch on top. the image needs to be really faint so that the scanner does not see the details of the previous work (play around with brightness and contrast on the initial scan. The initial scan is very important because after that, you can not add more data that the scanner didn't pick up, you can't just make data, so it has to be scanned in, and you can clean things up later in gimp). I have tried to do pen, even using very very 0.03 fin tip pens, but It still seems I get better control with a pencil. After that, I recommend looking into Vector art and specifically the program Inkscape, A vector is basically, drawing with shapes, so it is very clean. clean colors and clean lines. I draw by hand when prototyping a piece, but when I want to finish it, or make "Final lines" I use Inkscape. With Inkscape, I create a series of horizontally wide but very small circle shapes, these are going to represent the shape of the brush or pen stroke (like starting thin and going thick, but then thinning out again as I lift up the pen). By copying them, and then on the bezier curve tool, selecting the shape mode to be copied from clipboard, it will make a line, but instead of just a line, it will look like a brush or pen stroke, so it looks organic. Changing the shape of the stroke depending on how long or thick I want it to be, ie thick for the thigh, to more like a flick for details of the hands. I then do basically coloring (or basic fill colors) on various layers. To finish a piece I almost always use Gimp, however.
A last bit of detail, I find sometimes I need to reshape characters or features. The most absolute powerful way to reshape anything I find to be to use a 3D modeling program called Blender (free, but I recommend waiting 2 or 4 weeks till 2.80 is actually released since it will be friendlier to newer users), by making a plane, subdividing it to be many small squares, uv mapping it, and then using proportional editing to reshape the image, I can have more control over how an image can be edited unlike any other 2D editing program. If I want to shift the feet, I can box select the lower mesh, set to linear proportional editing mode, and move the feet, scrolling up and down to control the distance at which the effect extends (to the hips for example). If I want to adjust the elbow so that the arms look right, but I need to extend the distance out far enough that the arms still look straight, but this is also warping the chest, I can split the mesh (even remove parts) so that there is no direct connection to the area I am editing (think of like cutting a slit in the blank space of the drawing, so you could pull the paper apart, and the slit opens up), and this way effects only apply to the parts I want (making sure to be in connection mode only. I can go into more detail if you want.
Hopefully, you can glean something useful from my rambling.
