For example, I need to create a Mosaic to new raster with around 2000 files. Can I do this in model builder without clicking on each layer then selecting the tool?
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If all the rasters you want to add are in the same folder or workspace, then you can add the rasters as from Workspace and not just individual Datasets (right click on Mosaic, Add Rasters).
So you can use this tool in your model (Data Management Tools -> Raster -> Mosaic Dataset -> Add Rasters to Mosaic Dataset). The tool also has options for including sub folders to browse for raster datasets as well as using an input filter in case you want to filter the rasters by name.