Use the Cleanup tool in any of the following ways:
To clean up the background, click anywhere outside the drawing.
To clean up a paint region, click anywhere within the region. The affected pixels are painted in with the current Transparent color (shown in green below):
To clean up a part of a region, drag a bounding box around the region. The affected pixels inside the bounding box are inked in with the current Transparent color (shown in green below):
If you hold down Alt and drag a bounding box, the affected pixels outside the bounding box are inked.
Note, you could drag a bounding box around the entire drawing to clean it up. However, this is not advisable as some paint regions probably contain some details that you will want to keep.
To ink Transparent color over individual spots of dirt, place the Cleanup tool over the spots and click. The spots are inked with the Transparent color.
To ink a line with the Transparent color, place the Cleanup tool over the line and click. The line segment is inked with the Transparent color.