After merging all layers there should be one layer. In the tutorial I have added another plain white layer below it so that the linework shows up more clearly afterwards rather than showing up over the “transparent” backgound.
When you adjust the levels it should create a new layer. (unless that is not a feature on cs2, instead you can just make a new one but make sure it is above the linework layer.) After you have adjusted the levels to your liking, merge the linework and levels layer together. For adobe photshop cs2, instead of ctrl + alt + 2 it might instead be ctrl + alt + ~ when you are selecting the white areas of an image. (I think. I have only used cs2 for this kind of stuff once and I no longer have it on my computer to check sorry!) If all of the white areas around the drawing are selected, press delete. Setting mode to multiply should get rid of any really light shades of grey around the lines that may look like they are white against a darker colour underneath.
The reason for merging the layers is so that the image colours will only be a high contrast of black and white. If you don’t merge them and try to do this, the original scan underneath the levels layer will still be the original raw scan and it won’t work.
I think I should add too that if you scan in a PDF image and try to manipulate it this way it will most likely come up with lots of problems. (I haven’t figured out how to fix them sorry.) I usually scan in a super high DPI .tiff or .jpeg file depending on what I am doing with it.
Hope this helps! :)