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I would like to take a complex model with many joined object and slice the whole thing in into regular slices. I have tried Bisect and Ctrl R but that doesn't work on a joined object. Any help?

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You can use the Boolean modifier in intersection mode for this.

  1. Add a box (cube) the size of the desired slice
  2. Add a Boolean modifier to the object you want to cut into slices
  3. Position the box precisely on the slicing axis (Z in the example above).
  4. Duplicate the original object and apply the modifier to add a slice.

enter image description here

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You probably could benefit from useing knife project from different views (eg. Right / Top / Left / Bottom).

Please see this solution: Knife Project.

In your case you would have to just walk through these steps multiple times, until you have the sections that you need.

The movie ['The Cell' - released year 2000] used this effect to show the internal anatomy of a horse.

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