Automatic ways of Fixing non-manifolds

Before you get your hopes up too high, realize that these are not perfect solutions and may not even fix the non-manifolds. I always recommend manually fixing your model, but if you do not have the skill or time there are plenty of justified reasons to do it automatically. That being said perhaps you may just get lucky with the following methods:

1.) Netfabb

This is a free (need a Microsoft account) online service where you can upload your model to be fixed and within a few seconds receive a fixed version. This is probably the easiest and best automatic method.

2.) Meshmixer

This is a free program. What is nice about this program is that it lets you choose which non-manifolds it will fix individually. This can be done by going into "Analysis" --> "Inspector" , then this software will find non-manifolds:

• The blue balloons are hole non-manifolds. 
• The pink balloons are separate objects.  
• The red balloons are all other types of non-manifolds. 

You can click on the "Auto Repair All" to fix all the balloons at once. (Watch your model to make sure that the model does not change too drastically!)

You can also just fix individual non-manifolds by clicking on the balloons. If the balloon disappears then the problem is fixed. However if the balloon turns black, then the problem can not be fixed automatically. (Once again, watch your model to make sure that the model does not change too drastically!)

3.) Remesh / MeshLab

When there are lots of non-manifold errors, this is what I usually resort to. Your model will slightly loose the original shape, but usually it isn't too much.

To learn how to remiss a model see this post: Remesh Tool: How to Convert a CAD File

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