Sometimes when I use the Shift (m) tool, I get duplicate layers. Is there a tool to only select the top layers and delete bottom layers?
Sometimes when using the shift (m) tool, I delete out centers of objects, and then it creates multiple layers as duplicates. I must put a stroke on the top layer so that It can be cut out by my plotter. Well if there are duplicate layers, then all the layers get the same stroke, and then my plotter cuts multiple cut lines. Is there a tool to only highlight the top showing layers, and delete any duplicate layers underneath?
Sorry for the late answer.
There are two possible solutions.
1. Select the whole group ('Just Riding Around'), open Pathfinder panel and hit Outline button. This will eliminate duplicates (in this and similar cases), but also will remove the stroke. You can easily return it back hitting the '<' key (comma), which applies the last used color.
However, it'd require to completely ungroup and uncompound your artwork before running. 58 duplicates! More than those 4 you circled!
3. In your case, just select the group and hit Unite.
For operations like these using Pathfinder is way better than Shape Builder. Why the Shape Builder makes these empty paths in the first place, and does not have an option to kill them on creation automatically...