The simplest approach to avoiding more black discoloration to the furnace’s interior firebox is to avoid “sappy” wood such as pine and other evergreens. In this case, the burning wood isn’t the culprit; as sap burns, however, a sticky residue via the wood smoke coats the walls inside the furnace. This is the primary reason for the black buildup. The remedy: first, clean the chamber very well in the off-season with a mild detergent and wire brushes with stiff bristles. Next you’d want to start burning other hardwoods like oak, cedar, cherry or elm to keep from adding to the buildup problem.
The access window to the firebox is just as prone to getting black as the rest of the walls are, but you can’t take the same approach when cleaning it. After you’ve dealt with the problem with the rest of the firebox’s interior, you’ll need to wait for a time when the box is relatively warm – note that you’ll need a pair of heat-resistant gloves for this. Using a paint scraper on the window’s inner facing while hot will help scrape away the buildup without much fuss; however, never use a wet cloth to wipe down the glass or you’ll risk cracking the pane due to the drastic change in temperatures.
Wood placement may play a part in buildup reduction once you have the firebox sufficiently cleaned up. By laying the wood in a neat row perpendicular to the window, wood has a chance to burn more evenly; this cuts down on the chances of burning at a faster rate or producing an uneven burn, common when logs are placed sideways to the window or on their ends and sticking vertically in toward the roof.
While not necessarily life-threatening or damaging to the furnace, over time the black residue from burning, sappy wood will collect inside the walls or flue. This condition creates a backflow that will send smoke back through the vents and into the home. If your furnace has a large amount of buildup, check the vent pipes, chimney and flue as a general precaution.