Can we attack viruses by attaching proteins and such to their shells?
Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against rabies. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus.

The same is possible when you vaccinate against the surface proteins which a virus uses to dock to a cell. With the resulting antibodies this docking is at least hindered if not completely prevented. And there are interesting results from the Ebola research which used a small molecule inhibitor to identify the protein which is important for cell binding of the virus. It is called NPC1, when the receptor on the virus surface is blocked, no docking can take place. This will be one of the approaches to make a therapeutic. See here for more details.

And it is of course possible to design more of the molecules - the problem is to find substances which do not interfere with body functions or which stimulate other pathways.