Time to dispel a persistent misconception about Rapture.  While it may be optimized for short wavetables, it's not limited to them.  You can use the Rapture microhost for the following process (internal tempo, recording), or fire up your favorite DAW / sequencer.  Don't use a simple intrument track in Sonar.  BTW: I haven't found the top end file limit size yet.
 

• Export a drum track, stem mixdown, guitar pyrotechnics, or entire song to a .wav file. [Sonar:  File -> Export -> Audio ...]
• Load an instance of Rapture [Sonar:  Insert -> Soft Synth -> Rapture].
• Click on the Multisample window. Navigate to your exported .wav file, and load it into Rapture as a 'wavetable'.
• Add a middle C note [#60] to the MIDI track.  Extend it the whole length of your track / stem / mix. 
• Enable Write automation in Rapture's audio track automation lane(s).  Create an envelope or two [Ex. Sonar: Rapture 1 -> Filter 1 Cutoff 01 / Filter 1 Reso 01].
• Set up your filter of choice (continuing the single example) in Rapture.
• Begin playback, and move your Rapture GUI filter controls to write automation to the track.
• Bounce to Clip(s) or export the processed track again when you're satisfied with the results.

 
That's about it.  For some stutter and pitch-shifting effects, forego the middle C note and play it in live from a MIDI keyboard.  An octave above middle C will be double speed /pitch, and octave below will be half-speed/pitch, and so on.  Also good for DSP distortion processing, pitch envelopes, sequenced pans, etc. etc. etc.
 
Now think of what you can do with six Element processors in parallel ...

Actually, it was from reading your previous posts that I realized rapture can do more with longer samples. Good info. Not the most intuitive way to work with samples but good to know it is an option

Cool, B rock

Awesome tip Tom! 
 
If anyone is looking for some good stems to remix.  The current bleeding fingers competition stems from Hans Zimmer can be downloaded here:
 
http://www.hanszimmerwantsyou.com/
 
Could be fun to turn some of those brass stems into Rapture-ized drones. 
 
 

How would you do stuttering?
 
Suppose you keep pressed middle C so the song/stem is playing. And you want to stutter only the first beat/word/etc from a particular time (let's say refrain). How do you do that?
 
I tried assigning Sample Offset in the Mod Matrix to a slider. So I would go with the slider to the desired position in a song - but it's hard to hit the exact moment you want - and then repeatedly press middle C for the stuttering...
 
Any other suggestions?

First of all, that's an ingenious application.  Secondly, ... that's a tough one to answer.  You'll have me thinking about the best solution into the wee hours of the night.  I'm leaning towards an .sfz script.
 
Easy & obvious would be a snippet of the original clip loaded into an adjacent Element.  But that negates the spontaneity.  Hmmm.  Off the top of my head ...
 

I tried assigning Sample Offset in the Mod Matrix to a slider. So I would go with the slider to the desired position in a song - but it's hard to hit the exact moment you want - ...

 
That should be good up to about 10 seconds into the sample (at 44.1K).  If it were me, I'd probably preview the clip first in a sample accurate editor [Sound Forge; Audacity beta].  It would be easier to scrub to the exact stutter point.  Then make that sample value the maximum Depth value in the Modulation Matrix for the slider source.
 

... and then repeatedly press middle C for the stuttering...

My favorite trick for that is to make the Keytrack = 0 (under the Multisamples parameters).  Any key that you hit triggers the sample at the original pitch and rate.  So, you can use 2, 5, or ten fingers to cascade & roll the sample.
 
If the desired stutter rate is too fast for my technique, or requires machine-accurate spacing, then I cheat.  I use an onboard keyboard sequencer, 'note repeat' function, or a parallel hardware sequencer with a pre-programmed series of notes, and I trigger it while I'm playing.
 
No doubt you can do the same in software; something like Sonar's Matrix, <ahem> Project5 ... I'm not satisfied with these off-the-cuff "answers", so I'll let it simmer and try some stuff when I get back around my setup.

I wonder if the STEP GEN retrigger mode could come in handy for this application?  Use it on a tempo synced EG?
 

the STEP GEN retrigger mode could come in handy for this application

 
It does work.  More along the lines of a chopper/slicer than stutter sample repeats [AMP EG with an AR envelope; AMP StepGen with a high Step count, longer Sync cycle, and select retriggered steps].  Maybe in conjunction with the Sample Offset?  I need to explore this direction a little deeper.
 
Or perhaps I'm overthinking this one (again).  For example, triggering a delay line 'stutter' while dropping out the original sample signal?  Either way, "nice catch" with the StepGen retriggers.

It won't work.
 
If you stutter - let's say -  one word from a song, the playback has then to resume exactly from the point AFTER that word.
 
Sample Offset maxs out - as you pointed out - at 441000 samples, which is exactly 10 seconds from a track at 44100 Hz.
 
With the delay line - again - how do you resume the song after stuttering the fragment (word) ?
 
Slicer works and is easy to do.
 
But I thought Rapture might do what iZotope Stutter Edit does, so I wouldn't have to purchase that one :)