Replace mode is a tool that lets you carefully replace particles of one type with another, by simply drawing over the desired area. Particles of other types are simply left untouched. Specific delete is a tool that lets you delete a single kind of element. It works a lot like Replace mode but only for deletion.

Replace Mode

HUD Replace Mode

Ctrl-Alt selection looks like this.

1. Press Insert to toggle the mode. Your HUD should reflect that the mode has been enabled.
2. Hold Ctrl+Alt and select an element to be the "old" type. This is the type of particle that will get replaced.
3. Select another element to be the "new" type. This is the type of particle that will replace the "old" type.
4. Draw over anywhere to replace any occurrence of the "old" type with the "new" type.
5. Press Insert to exit Replace mode.

Here's a video showing how the workflow looks like.

Specific Delete

This is what specific delete looks like.

1. Press Delete to toggle the mode. Your HUD should show a notification that it was enabled.
2. Ctrl + Alt + left-click an element to select it with a cyan surrounding rectangle. This is the element that will be deleted.
3. Left click on a desired area to delete all particles of that element under your brush.
4. Press Delete to exit specific deletion.

Here's a short gfy on how it's used.