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Modifiers are toggle buttons that change how Align Pro measures a layer, rather than where it moves it to.
ModifierEffect
Align as GroupMoves the whole selection together as one rigid block, preserving each layer’s position relative to the others, instead of moving each layer independently.
Align to AnchorsUses each layer’s anchor point instead of its bounding box. Useful when a layer’s anchor has already been offset for another effect.
Align to MasksUses a layer’s mask shape instead of its visible content when calculating its bounds. Only affects layers that actually have a mask.

Some combinations are disabled

Align Pro greys out buttons and modifiers that wouldn’t produce a meaningful result together:
  • Align to Outside disables Align Horizontally, Align Vertically, Align Center, and Align to Anchors, since outside alignment only makes sense relative to an edge.
  • Align to Selection disables Align as Group, since you can’t align a group to its own bounds.
  • Align to Key Layer combined with Align to Anchors disables Align Left, Right, Top, and Bottom, leaving only centering, since an anchor is a single point with no distinct edges.
  • Align as Group disables Align to Selection, Align to Anchors, and every Distribute and Distribute Spacing button, since a rigid group has no relative spacing left to distribute.
  • Align to Masks disables Align to Anchors, since an anchor point doesn’t have a mask shape.
  • Align to Anchors disables Align to Outside, Align as Group, Align to Masks, and the four edge-based Distribute buttons (Top, Bottom, Left, Right). Centering and Distribute Spacing still work, since an anchor’s “center” is just its point.
If a control is disabled, it’s because the current Align to target or another active modifier makes it meaningless in that combination. This is expected, not a bug. See Troubleshooting.
You can set default modifiers and an Align to target for new sessions in Preferences.