Why does GIMP Clone copy pixels that are hidden by the layer I’m editing?

What Sample Merged Changes

The Clone tool has two different sampling scopes. With Sample merged disabled, the source is taken only from the active layer. With Sample merged enabled, the source is taken from all visible layers, producing pixels from the visible composite at the sampled position. A layer can therefore contain no copy of the pixels you see, while Clone still reproduces them because another layer contributes to the composite.

This does not mean hidden layers are included. The documented scope is the active layer alone, or all visible layers. A hidden layer is excluded from merged sampling. If the result appears to contain content from a hidden layer, first confirm that the content is actually visible through another layer, or that the source point and active drawable are different from what you intended.

Illustrative Exercise

Illustrative exercise: preserve an approved product composite and work on a test copy. Put a visible retouch layer above a product composite. The retouch layer contains the paint target, while the lower composite contains the product pixels you want to sample. Set a source with Ctrl-click on the desired layer before painting; GIMP requires an image source before Clone can paint.

Now compare two controlled cases. Case A has Sample merged disabled. Sample from the active retouch layer at a location where it has no useful product detail, then paint on that layer. The result should come only from the active layer, so the product detail from the lower composite is not used. Case B has Sample merged enabled. Use the same source and target positions on the test copy. The result can include pixels from the visible product composite because sampling uses visible layers together.

Pass condition: the observed difference follows the selected sampling scope, and neither case uses a hidden layer as a source. Stop the exercise if the source cannot be set or if the two cases use different source positions, because that would confound Sample merged with source selection.

1. Duplicate or otherwise preserve the approved original before testing.
2. Select the drawable that should receive the cloned pixels.
3. Set the image source with Ctrl-click on the intended source layer.
4. Record whether Sample merged is enabled.
5. Paint a small test mark and compare it with the visible composite at the source position.
6. Repeat on the test copy with the other Sample merged state, keeping the source and target locations consistent.

Choose the Correct Branch

Use Sample merged disabled when the correction must draw only from the active layer. This is the appropriate branch when the active layer contains the approved texture or retouch material and lower visible layers should not influence the repair.

Use Sample merged enabled when the source should represent what is visibly assembled across layers. This is useful when the product appearance depends on several visible drawables and you want Clone to sample their combined visible result. The visible composite is the scope; hidden layers remain outside it.

If changing Sample merged does not explain the result, do not alter alignment or masks as a first response. Editorial diagnosis: check the source layer selected by Ctrl-click, the active target drawable, and whether the suspected pixels are actually visible. Alignment controls how the source offset behaves across strokes; they do not define whether sampling uses the active layer or visible layers.

Verify Before Committing

After choosing the branch, paint a small test area on the test copy and inspect the pixels against the intended source. The acceptance condition is precise: Sample merged disabled must use only the active layer, while Sample merged enabled may use all visible layers and must exclude hidden layers.

If the test passes, apply the same setting to the working correction and keep the approved original unchanged. If it fails, stop before broad painting and recheck the source drawable selected with Ctrl-click, the active target, and visibility. Clone can target another drawable, so the layer receiving paint is not necessarily the layer supplying the source.

Use this question’s review worksheet

The sample rows are fictional exercise data. Preserve the example, save a working copy and record your own inputs, observations and decisions. The example is not a test receipt.

Fictional/manual Clone sampling worksheet (CSV)