Sorry that is what I meant, it will not allow me to use 'select by attribute' or 'eliminate' on many of the layers in my model. It will not allow me to connect them as 'Input tables' but it will allow me to use them to specify 'cell size' or 'mask' which is stupid as these layers are polygons not rasters.
I can go into the tool and tell it to use any layer in the table of contents, BUT it doesn't connect to where it already exists in modelbuilder, it creates a new icon for it and starts a separate model in modelbuilder which is definitely something I don't want it to do. No one has had this problem before?