Merged visible layers ignore layer mask visibility

Answer

GIMP's Merge Visible Layers command does respect the visibility of layer masks: it first applies each mask to its layer’s pixel data, then copies the resulting visible pixels to the new merged layer. The masks themselves are discarded after the merge, so the final layer contains only the flattened pixel values.

When the mask appears ignored

• The layer’s eye icon is off (the layer is hidden). In that case the layer contributes nothing to the merge, which can be mistaken for the mask being ignored.
• The layer is inside a layer group whose visibility is off, producing the same effect.
• The image mode is Indexed; merging may dither or reduce colors, making mask effects look different.

Steps to verify mask‑aware merging

1. Create a new RGB image.
2. Add two layers: a bottom layer filled with solid color, a top layer with a different color.
3. Add a layer mask to the top layer (e.g., a gradient from black to white).
4. Ensure both layers are visible (eye icons on).
5. Choose Layer → Merge Visible Layers.
6. Inspect the resulting single layer: the transition should match the on‑screen preview.
7. If the result looks different, check that the top layer’s eye icon is on and that no parent group is hidden.

Forcing mask‑aware merging

No extra option is needed; the command already uses the visible state. If you need to keep the masks after merging, duplicate the visible layers first (Layer → Duplicate Visible Layers) and then merge the duplicate, leaving the original masked layers intact.

If you suspect a bug, provide the image mode (RGB/Grayscale/Indexed) and whether any layer groups are involved; that detail changes the recommendation.