Make the object part of an entity. For plants and stuff, use a func_illusionary, then it will be non-solid. For fences, add a CLIP for to block players. func_wall will also work but it is super-solid, blocking EVERYTHING including bullets. For most partially transparent objects, you would want bullets to pass through.

Whatever you make it, set the properties like this:
RenderMode = solid
FXAmount = 255

This will make the black/blue parts invisible.

This works on many visible entities like func_wall, func_door, func_illusionary, func_breakable etc. etc.