I made some actions to run Image Doctor from Quickmask mode (in Photoshop). I find this to be an easy way to run the filter when I have a lot of scratches or blemishes to clean up.

The way it works, is I first go into Quickmask mode (Q) in Photoshop (make sure you do NOT have a selection made).

 

Once in Quickmask mode (see red circle in first figure), I can use the brush tool (green circle in figure) to paint along a scratch or blemish. Think of the red paint as the selection you are making. Tip: use [ and ] to change the radius of the brush. Then run one of the actions (for example, the "Scratch" action. After applying the effect, the action will bring you back to Quickmask mode so you can make more selections. It is best to work iteratively (one small section at a time) rather than making one huge selection. That is the nice thing about doing it in Quickmask mode.

You can use this same Quickmask mode technique to remove pimples or dust particles one by one. Also, skin softener can be applied in the same step by step method. The action set includes actions for all of these these techniques.

Notes:
You can run the action with a keyboard shortcut by double clicking on the action and setting the "function key"

You can make the action interactive (so you can adjust the filter settings) or not by activating/deactivating the option next to the name (green circle in the second figure). If you get an alert dialog saying the toggle state of all dialogs in this action is undoable, don't worry about it; you can just click the button again later to bring it back.

The action is doing the following steps: 1) exit Quickmask mode, 2) run the filter 3) deselect all 4) back to Quickmask mode

 

Installing the actions
You should be able to double click on the actions to import them or use "Load Actions" from the actions palette (red circle in figure). Here is the action set: