Most coffee makers are cleaned by filling the reservoir with undiluted white vinegar (3 cups). (Do not add coffee.) Remove the water filtration disk if you use it before starting. Then start the brew cycle as if making a cup of coffee (including putting a paper filter or the permanent filter in the filter basket and close the lid). Put a decanter on the warming plate. After brewing, turn off the coffee maker and let stand for 30 minutes. Run another cup of vinegar through the coffee maker. Take the decanter filled with vinegar and discard the liquid (pour down the sink drain). Rinse the decanter. Fill the reservoir with clean water and put in a new paper filter (or clean the permanent filter and put it back). Again do not add coffee. Run a brew cycle to rinse the unit. Discard the water that is in the decanter after the brew cycle. Do a second clean water only brew cycle (with new empty paper filter or permanent filter after cleaning again). However, if you notice an odd taste, repeat the rinse cycle.
You can alternatively use the Mr. Coffee Coffee Maker Cleaner (mix as directed on that package). In either case, this removes mineral deposits (calcium from hard water). For soft water, the cleaning should be done every 80 brew cycles. If you have hard water, do this every 40 cycles.
The manual is available from www.mrcoffee.com/Product.aspx?pid=121
, if I have the correct product version. For some reason this site isn't coming up for me today. Check the manual to find out if there is any specific details for cleaning that aren't shared with other Mr. Coffee products.
I hope this helps.