---
title: Clean up 2D and 3D
url: https://www.moldraw.com/docs/drawing/how-to-clean-up-2d-and-3d-structure-drawings/
section: Draw structures
updated: 2026-10-20
publisher: LabCanvas
---

# Clean up 2D and 3D

> Click Cleanup structure (the magic wand on the Home tab) to even out bond lengths and angles. Select part of the drawing first to clean only those molecules. Press Shift+Ctrl+D for 3D Clean Up, which shows the molecule in 3D perspective on the canvas.

1. Select a molecule if you want to clean only that one. With nothing selected, the whole drawing is cleaned.
2. Open the **Home** tab and click **Cleanup structure** (magic wand icon) in the **Cleanup** group.
3. Check the result. Press `Ctrl+Z` if you want the old layout back.

## Where to find it

| Action | Where |
| --- | --- |
| 2D clean up | **Home** tab, **Cleanup structure** button. On a phone the tile is **Clean up**. |
| 3D Clean Up | **3D clean up** button next to it, or `Shift+Ctrl+D` (`⌘+Shift+D` on a Mac). The phone tile is **3D clean**. |
| Both | The [command palette](https://www.moldraw.com/docs/settings/how-to-use-the-command-palette/) (`Ctrl+K`): type "clean". |

2D clean up has no keyboard shortcut. Use the button or the command palette.

## What 2D clean up changes

- Bond lengths become equal. It uses the bond length from **Settings**, **Bonds**.
- Bond angles and ring shapes are tidied. Fused rings get regular shapes.
- Only atom positions change. Atoms, bonds, charges, labels, lone pairs and colours stay the same.
- Each molecule stays where it was and keeps its heading. Clean up does not mirror a molecule, so wedges keep their meaning.
- Chair and boat rings keep their shape.
- Lone pairs move into the free gaps between bonds. Their dot or line style stays.
- Arrows, text and shapes do not move. A reaction scheme stays in order.

## Selection only or everything

With a selection, clean up works on each molecule that the selection touches. Other molecules do not move at all. This is useful in a [reaction scheme](https://www.moldraw.com/docs/reactions/how-to-make-a-chemical-reaction-scheme/) where you only redrew one product.

With nothing selected, every molecule on the canvas is cleaned. Each one stays in its own place.

## 3D Clean Up and Structure Perspective

3D Clean Up builds a real 3D shape for one molecule and draws it on the canvas in perspective. This view is called Structure Perspective.

1. Select the molecule you want. With no selection, the newest molecule is used.
2. Press `Shift+Ctrl+D`. The drawing gets a 2D clean up first, then the 3D pose appears.
3. The **3D View** tool turns on. Drag on the canvas to turn the molecule.
4. Use the **Fade** slider to set depth shading. The triangle button turns on **Depth taper**, which makes far bonds pointier.

While the 3D pose is on, three buttons change their meaning:

| Button | What it does in 3D mode |
| --- | --- |
| **Cleanup structure** or **3D clean up** | Re-minimizes the shape in 3D and keeps your current view angle. Use it after you add atoms. |
| **Flatten 3D pose** | Writes the pose you see into the 2D drawing and leaves 3D mode. |
| **Exit 3D mode** | Drops the pose and shows your original 2D drawing. |

`Alt+D` switches the **3D View** tool and depth shading on or off. For the separate 3D panel on the right, see [3D viewer](https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/).

## Clean up while you draw

**Settings**, **General**, **Drawing**, **Auto-layout after bond burst** is on by default. When you add several bonds quickly, MolDraw tidies that molecule with the same engine as clean up. Turn it off if you want full control of every position.

## Common problems

| Problem | Fix |
| --- | --- |
| "Nothing to clean up" | The canvas is empty. Draw or paste a structure first. |
| Cleanup is skipped for an organometallic sketch | Drawings with a tilted Cp or arene ring and metal to centroid bonds are left as drawn. Arrange them by hand. |
| Cleanup takes too long | Wait a few seconds and try again. On a very large structure, select one part and clean it alone. |
| Only one molecule changed | Something was selected. Press `Esc` to clear the selection and run it again. |
| 3D Clean Up shows the wrong molecule | Select the molecule you want before you press `Shift+Ctrl+D`. |
| A molecule from a crystal or framework lattice does not go 3D | Framework lattices use their own template, so 3D Clean Up skips them. |

For chair rings and Newman views, the [chair conformation guide](https://www.moldraw.com/blog/chair-conformation-newman-projection-guide.html) explains the shapes that clean up keeps.

## Questions and answers

**Does Clean up change my wedge and hash bonds?**
No. Clean up only moves atoms and never mirrors a molecule, so wedges and hashes keep the same meaning.

**Can I clean up only one molecule in a reaction?**
Yes. Select that molecule, then click Cleanup structure. The other molecules do not move.

**What is the shortcut for 3D Clean Up?**
Press Shift+Ctrl+D, or Cmd+Shift+D on a Mac. Drag on the canvas afterwards to turn the 3D pose.

**How do I go back to the flat drawing after 3D Clean Up?**
Click Exit 3D mode to drop the pose. Click Flatten 3D pose to keep the projected shape as a new 2D drawing.

**How do I undo a clean up?**
Press Ctrl+Z. The old positions come back in one step.

## Practice it

- Interactive lesson: [How to clean up a chemical structure](https://www.moldraw.com/learn/how-to-clean-up-a-chemical-structure-drawing/)

## Related pages

- [3D viewer](https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/)
- [Rings and structures](https://www.moldraw.com/docs/drawing/how-to-draw-benzene-cyclohexane-and-fused-rings/)
- [Select, move and align](https://www.moldraw.com/docs/drawing/how-to-select-move-copy-and-align-structures/)
- [Settings reference](https://www.moldraw.com/docs/settings/moldraw-settings-reference/)