How I think they did it was by using both Thermite and explosives a double whammy if you like; If you take the lower larger bulkier columns, which were basically large sealed boxes, all you need to do is fill these voids with thermite plugs every so often and ignite these first, this would burn from the inside outwards and then only a smaller charge is needed to cut the rest of the way through the remaining of the jacket/layer of metal, this would also account for the melting pools of metal found at the sub levels where most of the large columns/bulk of steel came to a rest, IE, the molten debris found was actually channelled down the inside the lower columns themselves.
If you look at the building being reduced you can clearly see they are being taken down from the bottom upwards and the outer walls were left intact to act as a collecting funnel, then as the internal voids is filled to capacity, only then does the outer facades begin peeling outwards as it went, this would also help to mask any charges from being seen at the very beginniing, and not seen after as the dust cloud gathered and got larger.
Again, it looks like a top down demolition but is actually quite the reverse, this is why most of the steel was found at the sub level and left no huge pile of debris above ground.
The concrete floors were ground up in between all the beams, and remember as the towers rose their superstructure got less bulky, IE, smaller and smaller beams as it rose, this absolutely points to a bottom up clearing model, which looks like a top down but is not.