I frequently mark up my clips, select all markers, and make subclips (all at once). I'm doing this with long audio files at the moment to generate soundbites in the form of subclips. The problem is that the auto-naming scheme starts at 1 and counts up. If you have more than 9 subclips, they no longer alphabetize chronologically, and I have to rename them all manually.

So, I get:

1
10
11
12
...
19
100
101
...
2
20
21
(etc)

At the moment, I rename them all manually to get:

001
002
003
(etc)


Is there a way to auto-rename them all intelligently!? this is driving me nuts!

Just an idea: did you try the mac os x Automator? If I am right, in this kind of "nuts me crazy" jobs the Automator is a great tool. However, I am not expert in this regard, so I can not give you a script

Sure, after Automator, you have to add those clips again to FCP.

Yeah, so the clips are virtual. I can export them as actual files, batch rename them, and then re-import them, but the nice thing right now is that they exist only as metadata.

Ah Gyula did answer but he left it open because he didn't want to insult your intelligence, Eric.
The easiest way is to use Automator to batch rename your actual media files then batch rename in FCP browser filename to clip. And because I don't want to insult (intimidate or 'down put') you yet again, I'll let you figure out how to do that.
FYI for future reference, just add two zeros after the clip name you choose. It is weak that FCP doesn't add the functionality but most editors use the take numbers as reference for each clip. They also choose which take it good etc.
This is all for master clips only. Subclips are a different beast.
With the way you work with markers then making them subclips, it should be chronological from the marker names no?
For your present projects I'd say export the batch list then edit in Excel and reimport and reconnect to media.