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Use soft edges

The padlock at the right of the palette strip is the opacity lock, and it is on by default. While it is on, every pixel you paint is either fully there or fully erased -- nothing in between.

Turn it off

Click the padlock. nfty explains the trade-off once, and then the A (alpha) slider beside it becomes active. Paint at any opacity you like.

Why it is locked in the first place

Partly-transparent pixels have no correct answer when art is converted into a 3D voxel model: a converter has to either drop the pixel or make it solid, and neither is what you drew. The lock is there so you opt into that knowingly rather than discovering it later.

Partial alpha is legal -- nfty will cook it, ship it and never complain. It is a decision, not an error.

Erasing is not the same thing

Erasing works normally whether the lock is on or off. That is how a layer gets its shape, and layers have to show through each other.

Check a finished project

nfty inspect yourbook.cbk --voxel

Lists every variant carrying partial transparency, and how much of it. Worth running before you hand a collection to anyone planning to make models out of it.