The only thing you can make is the brushes. Using the brush on a fossil is supposed to trigger a mini-game, according to the official wiki. The tools are part of the mini-game, and which tools are available to you depends on the type of brush you have.
In any case, I managed to get it working. It looks like somehow I was truly not standing close enough - placing my character directly on top of the fossil then using the brush caused the mini-game to open at last. I succeeded in getting my first fossil (an unidentified torso).
Collecting them is enough for me. Remember, there are several
types of gamers. Some are motivated by discovering and collecting new things - I am one of those (a combination of the achiever/explorer types). Once I run out of things to collect/discover, I tend to lose interest in a game. So the more collections are possible, the more I want to play. Not everyone is motivated by combat, efficiency, and things like that. Hence why I got so annoyed when I discovered the erchius mine mission was mandatory before I would be allowed to explore/collect - they forced gamers like me to engage in the type of gameplay we don't like, before we were permitted to engage in the type of gameplay we *do* like (and which Starbound is full of, it's just gated behind that stupid quest).