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Megadeus
Definitely use the specific software made for you scanner. If your software has different modes use whatever is least automatic, usually "expert" or "manual."
Look for an option labeled something along the lines of descreen or moire removal and make sure it's enabled. Sometimes this will be available in the document type selector labeled magazine along with other options such as film, line art and text.
If your scanner has a white lid backing, place a piece of black construction paper directly behind the page you're scanning to reduce ghosting from the other side of the page.
Post processing can only correct color so much before it starts to look awful so do as much color correcting as possible at the scan stage. Do a quick and dirty, preview scan, remove the page from the scanner and compare the color between the preview and the original. Adjust the color and brightness to as close to the original as possible, being especially cautious not to blow out the highlights (when the white spots start to blend with surrounding near-white colors). Then, replace the page and rescan.
Various sources will be printed at different DPI levels. Try test scanning at various DPI settings to find which ones work best. You can select a small portion of the image in the preview window to speed up this process since it only has to scan a small portion.
Also (system memory permitting) try scanning at a ridiculously high DPI level, such as 600 or more, and then resize it down to half. This generally removes some noise but it's a bit of a trade-off because the most powerful tool in your arsenal, the scanner's built-in descreening filter, usually starts to loose effectiveness as you approach 300 dpi and beyond 350 is generally worthless.
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