For many years I have stored my figures in A4 sized Filing Boxes. I make sure that I buy ones which do not have holes in them (as some do to facilitate taking them off shelves). These are cheap ones which I bought in packs at the UK Stationery store, Staples.
The first thing I do is to remove the clip which is inside the box for holding paper down. This involves pulling the spring out with a pair of pliers, then trimming the plastic clip off with a modelling knife. Some of my older boxes had metal clips but whatever the system was then I removed them.
I then stretch a piece of flat elastic across the back of the box and staple it into place with a staple gun. On the new (flimsier) boxes, the staples protrude at the back so I push them flat, which makes them more secure anyway.
I then fill the box up with figures, as in this one which contains all 15 battalions of the British Army at Culloden, plus their 5 Brigade Commanders, 2 Line Commanders (with their ADCs), the Duke of Cumberland (plus his ADC and Standard Bearer), and Cumberland’s Escort of 2 Hanoverian Hussars.
The elastic across the back of the box is used to hold Command Sabots (as in the box above), or Artillery Deployment Bases, as in this one, which contains British Cavalry, Artillery, Argyll Militia and Lowland Volunteers. In the days when we moved around the world a lot, I would pack tissue paper on top to stop transit damage.
Finally, I label the boxes, both on the top and one end. The latter is essential due to the way in which I store them on shelves in a built-in cupboard in my study. Because they are in stacks, I can easily identify each box. There are actually 24 boxes on that shelf, four in each stack, two stacks deep and three stacks across. To get at the rear ones, I just swing the front ones outwards.
I currently have two shelves full of completed figures in boxes. The third shelf, and the area to the floor below that, is full of figures in their original manufacturers boxes, awaiting modelling and painting. I put similar sets into shoeboxes, and label them. I also have a shoebox containing plastic bags of figures which have been sorted, but not yet painted.