I am running a model that has multiple layers (3) going into a clip tool. My output (as expected) is three layers. This is the final process for 2 of the layers but I want to continue with some processing on the third layer. How am I able to continue the geoprocessing on this third layer. Every time I connect it to a new tool I get all 3 layers and I can't delete them out of the dialogue.
Create those 3 layers. Then in your model add the Select Data tool from ModelBuilder>Insert>Model Only tools>Select Data. For the input Data Element select the workspace it is creating the 3 layers and then for child data element choose the layer you want to iterate over. The three layers must exist for the first time to set up this tool correctly.