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My personal Lego storage system.

2011: new storage system, similar to the one you can see on the pictures page but newer and made of plywood instead of MDF. Here before the final sanding and varnishing, with a small Technic Telehandler for scale
Lego storage tray made of wood

More pictures: my desk is completely covered in Lego. There's two trays each 400x600mm, three at 300x600, plus a couple of 100x600 deeper bins along the back.

Detail of one tray, mostly just showing the mix of 7mm and 4mm plywood used for dividers. I buy cheap 7mm plywood in 1200x2400mm sheets and it tends to bend as it dries, so the 7mm dividers are solid enough to accept nails that hold it flat while the glue dries. 4mm ply is cheaper.

Shelves to one side of the desk with plastic boxes of parts and work in progress models.

Underside of a tray showing the nails that hold it together during assembly. BTW, I do have to drill a 1.5mm hole for the nail otherwise the ply splits when I drive the nail.

And the box of extra parts.

Building the trays is relatively straightforward since I have the tools. I have a small table saw so I can cut straight and parallel easily. I bought a sheet of 7mm plywood (1200x2400mm), and a smaller sheet of 4mm plywood (900x1800mm?), then cut six 400x600 baseplates (one to go on top of the stack if I need to move them). The rest got sliced into 50mm wide and 80mm wide strips, and so did all the 4mm plywood.

I built the trays one at a time so I could experiment with bin sizes (if I got it wrong the next one would be better). I usually have at least a rough idea of how I'm going to use the tray, and for my "axles and gears" tray I had a very detailed plan of where each part would go. So the 12 axle compartment is 12.5 studs long, for instance, even though the rest are usually about 10.5 x 8.5 studs (or smaller).

To make a tray I cut the outside strips to length first and trim them to exactly match the baseplate. For the first one I slotted the baseplate to accept the main strips, but that didn't really help so I didn't bother for the rest. One baseplate was so warped that I used an extra strip of 7mm ply from the very start, glueing and nailing that frame before attaching it to the baseplate. I use PVA wood glue, it's safe to handle and dries slowly enough that I can correct mistakes.

Once the basic frame is in place I start cutting the main dividers. For the shallow trays that's 5 or 6 strips the full length go in, often spaced at 8.5 or 10.5 stud intervals (so they take 8 or 10 stud parts). They are glued in place rather than nailed and glued. I haven't had one fall out, and once the glue dries I've had to break the wood to geth them out. Try to avoid that :)

I don't stop to let the glue dry during assembly - part of the purpose of the nails is so I don't have to. After the long dividers I cut the short cross-dividers and glue them in one at a time. This is the point where I often have a few longer Lego plates or bricks to use as measuring guides.

Once the tray is physically assembled I wait a day or two for the glue to dry, then varnish it. Usually I try to use a waterbased varnish, but this time I got some mineral stuff cheaply so I've used that. It's not too bad, I have a filter mask (which I bought for welding dirty stuff) and "organic" filters for it that mean I can barely smell the solvent. I have disposable gloves for working on bikes, and they work for painting too. Then I leave it a week for the varnish to dry and stop stinking, moving the trays out to a sunny spot once they've has a day to become slightly more than touch dry. With the mineral-based stuff the stink persists for a week (I learned that the hard way - had to empty the Lego back out of a tray so I could leave it outside to stop stinking.

Right now all my Lego is in four boxes. OK, four boxes and a few extra bags - I got the Lego touring truck after I packed the boxes, so there are some extra sets. And some pieces I found while packing everything else up. Anyway, within the boxes everything is sorted as below, but in ziplock bags. About 200 ziplock bags, to be precise :)

My collection is mostly Technic, with some ancillary parts. There are a lot of yellow bricks sorted into gallon plastic cake box things, one each for smaller than 1x6, 1x6 or longer, 2x2 and 2x3, 2x4, bigger than 2x4, 2x2 and 2x3 not yellow, and 2x4 and bigger not yellow. There's also one of those with odd bits in it - Technic turntables, digger buckets, link-based tracks and chains, and so on.

There's a Mindstorms box full of wheels and tyres, but this is inside one of the four boxes above. It's just convenient to have them held separate.

I sort parts into groups that roughly fill one of the 3x3x3" compartments in the larger Technic boxes. This is because I build wooden trays with that size compartments in them :)

So I have groups for things like 1x1x1 Technic bushings, or 2x2 yellow L plates. I sub-sort by colour, but only when there is a single part that needs to be partitioned. I also mix disparate elements - I have gears and axles in the same bin because it's easy to find either element in that combination. For instance, 5 long axles go with 40T gears, and 2x1 bricks with cross hole go in the 8 axle bin (because that bin is 12 and a bit long (there is a row of three across the tray, with 10/12/8 axles in them)

Naturally I have a few bins of assorted parts, and some parts are in larger bins - I have a single "trench" bin in one tray full of Technic 1x16 beams, for example. Custom built containers have advantages in this respect. Mixed parts I tend to go either for disparate parts as above, or related parts - all my angled axle joiners are in one bin (the #1..#5 ones).