It is not hard to make a good box or case for tools or instruments. And you can often improve the usefulness of an existing box by judicious addition of foam or flaps. By foam, I mean closed-cell polyethelene packing, not to be confused with styrofoam. Styrofoam is weak and crumbly; closed-cell LDPE (low-density polyethylene) is tough and durable. I have a socket set where I replaced the vacuformed insert with LDPE nearly 20 years ago. After years and years of use, with hundreds of removals and re-insertions, the foam is still resilient, still grips the tools, and is ready for decades more.
Step 1: Getting Started
What you need: box or case, foam, felt tip marker, art knife, hot-melt glue.
Sometimes needed: cardboard, paint.
Plug the glue gun in so it can heat up while you think.
Closed cell foam is saved from appliance or equipment boxes. LDPE is what you want. It's easy to glue in place, and very easy to cut. If you don't have a single piece of foam big enough to fill a particular area, you can glue smaller pieces up to fit.
Step 2: The Case of the Upgraded Dremel
This is a Dremel case. I added bit-holder foam, sockets for a couple more accessories in the lid, and a cardboard cord-retainer flap.
Step 3: Hold-downs
When you have layout options, lay the tools or other objects in trial arrangements till you find one you like. For heavy tools, allow for proper cradling; think about how the weight will be supported, especially when the case is closed and sitting upright.
Sometimes after an object is well cradled from sides and below, it needs to be braced from above by a foam block glued to the box lid. In this case, make the best measurement possible for the required thickness of foam, cut it just a bit thicker, set the foam on the object, apply glue to the top of the foam, then close the lid on it. After a minute, open the lid; the foam should be firmly glued, and in the right place. Now when you close the lid, the foam clamps the object in place.