Where Digital Clear Aligner Treatment Plans Lose Precision - and What We Can Do About It
- Jesper Hatt DDS
- Dec 13
- 5 min read
Reflections on data loss, clinical reality, and predictable outcomes in clear aligner treatment
When the plan looks perfect - until it isn’t
The digital plan looks flawless.
Movements are smooth. Attachments are well placed. Staging appears conservative and biomechanically sound.
Then the patient starts wearing the aligners.
Within a few weeks, we see it: tracking issues, unexpected rotations, attachments don't track, refinements creeping in earlier than planned.
We’ve all seen this. And most of us have asked the same question at some point:
“What went wrong — when everything looked right on screen?”
In many cases, the answer isn’t biomechanics, compliance, or even case selection.
It’s something far more subtle and far more underestimated:
Data loss across the aligner workflow.
The digital promise and its quiet limitations
Clear aligner treatment is built on a digital chain.
Every step depends on the integrity of the data before it.
In theory, this should give us precision and predictability. In reality, each digital handoff introduces small deviations - and those deviations add up.
What looks like a single “digital workflow” is, in practice, a sequence of separate systems:
Intraoral scanning
STL file generation
Aligner planning software
Tooth segmentation
Staging and movement algorithms
Export to third-party software
3D printing preparation
Resin behavior
Thermoforming and trimming
Each step can subtly alter the original data.
Individually, these changes seem negligible. Collectively, they can influence aligner fit, force expression, attachment engagement, and ultimately predictable outcomes.
From scan to STL: already the first compromise
The intraoral scan is our foundation.
But even here, the data is not a perfect replica of reality.
Scanners reconstruct surfaces using algorithms that simplify geometry.
Undercuts, sharp edges, and complex gingival contours are often smoothed or approximated.
Once exported as an STL file, we lose additional information:
No color data
No material properties
No biological context
The STL is a mesh - not anatomy.
This doesn’t make it unusable.
But it does mean that every downstream decision is based on an approximation, not the mouth itself.
Segmentation: where biology meets mathematics
Tooth segmentation is one of the most critical - and least discussed - steps in aligner planning.
Software must decide where one tooth ends and the next begins.
It does this mathematically, not biologically.
In many systems, segmentation involves:
Smoothing of boundaries
Interpolation where data is unclear
Algorithmic assumptions about root orientation
Small inaccuracies here influence everything that follows:
Center of rotation
Force vectors
Attachment effectiveness
Interproximal contact behavior
What looks perfectly segmented on screen may already be a simplified version of the truth.
And once segmentation is done, that version becomes “locked in.”
Staging and movement planning: precision vs. realism
When movements are staged, we often focus on how much a tooth moves per aligner.
Less attention is paid to how accurately that movement is transferred into a physical aligner.
If treatment steps are exported to a third-party system. Which is common in in-house or fragmented workflows - additional processing occurs:
Re-meshing
Resolution adjustment
File conversion
Slicer optimization
Each step can slightly alter surface detail and geometry.
Again, nothing dramatic.But aligners don’t work in millimeters - they work in tenths and hundredths.
What looks perfect on screen rarely behaves the same in the mouth.
3D printing and materials: when physics enters the chat
Once the digital plan becomes a physical model, we leave the world of pure software.
Printer calibration, layer height, and resin behaviour now matter.
Different resins shrink differently.
Some are more dimensionally stable than others.Temperature, curing time, and post-processing all influence the final model.
Even with an accurate printer, the printed model is not identical to the digital file.
And when aligners are thermoformed over these models, another variable enters:
Material thickness
Elastic recovery
Pressure distribution during forming
To truly calculate aligner thickness and force delivery, the software would need to be calibrated to the exact thermoforming setup.
In practice, no in-house system can fully account for this.
Trimming and finishing: the final invisible variable
Laser trimming or mechanical cutting of aligners requires specialized third-party software.
Trimline positioning affects:
Attachment engagement
Gingival margin interaction
Aligner seating
Once again, data is interpreted, translated, and executed by another system.
At this stage, even minor deviations can influence comfort, retention, and tracking - especially in more complex movements.
What many of us underestimate
Most clinicians don’t ignore these issues - we simply don’t see them.
The digital interface is clean, confident, and convincing.
It gives us the impression of control.
But the reality is this:
The more fragmented the workflow, the more opportunities for cumulative data loss.
This doesn’t mean in-house or smaller lab solutions are “bad".
It means they are best suited for simpler treatments, where small deviations don’t compound into clinical problems.
Complex cases demand tighter integration.
A collective realization
Many of us have discovered this the hard way - through refinements.
More refinements than expected
Attachments that don’t behave as planned
Movements that stall despite good compliance
As clinicians, we know refinements aren’t failures.
But we also know that excessive refinements are signals.
Signals that the digital plan and the clinical reality weren’t perfectly aligned.
A note from the literature
Empower your practice and deliver the exceptional care your patients deserve.
If you’d like to dive deeper into this topic - from digital setup to biomechanics and patient communication - you’ll find practical, step-by-step guidance in our book, Mastering Aligner Orthodontics.
The book covers how digital decisions influence force systems, attachment design, button placement, elastic use, and how to reduce unnecessary refinements in daily practice.
Click the link below to get your copy today!
Why integrated systems matter
Large aligner manufacturers use closed, fully integrated systems.
From STL intake to aligner production, the software environment remains consistent.
Data isn’t repeatedly exported, reinterpreted, or rebuilt.
This doesn’t eliminate all inaccuracies. But it dramatically reduces cumulative data loss.
That’s why these systems tend to deliver higher predictability in complex cases.
Smaller labs and in-house setups don’t have that luxury.
They must rely on fragmented tools - often excellent individually, but disconnected as a whole.
Bridging the gap: where AlignerService fits in
That’s exactly why we built AlignerService.
Not to replace your clinical judgment.
Not to oversell digital perfection.
But to help clinicians bridge the gap between digital design and clinical reality.
By working within tightly controlled workflows, focusing on biomechanics, attachment design, button placement, elastic use, and refinement reduction, we aim to minimize the weak points where data loss tends to occur.
The goal isn’t fewer steps on screen.
It’s more predictable outcomes in the chair.
Closing thoughts
Digital aligner treatment is powerful - but it’s not magic.
Precision doesn’t come from software alone.
It comes from understanding where digital models fall short, and compensating for that clinically and technically.
You stay focused on your patients.
We handle the digital complexity - safely, efficiently, and with the precision your reputation deserves.
Free case selection assistance
Increase your clinical confidence with complimentary case selection and expert treatment planning support. Within 24 hours an expert dentist will send you an indexation of whether your case i easy, moderate, complex or should be referred to an orthodontist. Try it out today - click the button and follow the instructions.
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Kind regards
Jesper Hatt DDS
P: +41 78 268 00 78
AlignerService
We are dentists helping dentists create realistic, safe and predictable treatment plans with clear aligners.
Currently more than1500 dental practices in 19 different countries use our service on a regular basis. We offer expert guidance in the following clear aligner systems: Invisalign, SureSmile, ClearCorrect, TrioClear, Angel Aligners and Spark.
AlignerService is a preferred partner of ClearCorrect and TrioClear.
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