Using FamilyTreeMaker - I would attempt to solve your problem in the following way.
Create a new file and copy into it only those people you want to appear on the chart.
Publish an Extended Family Chart (which charts everyone on the tree connected to the selected individual) and see how it looks - probably a mess with little sub-trees with one or more duplicated individuals from the main tree. There will be differences depending on who you choose as the starting individual. All people with the same generational separation from that person will be at the same level on the chart.
For the individuals that are duplicated, change the order in which they appear as children in their family. For example, John Smith the 3rd of 4 children marries Ann Brown the 2nd of 6 children - move John to 4th in the list and Ann 1st in her list. This may reduce the number of separate sub-trees but is unlikely to remove them all.
Start moving the sub-trees to more suitable places on the chart: [Before you do, make sure all your settings are in place - anything changes cause the chart to regenerate which will restore everyone to their original position].
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Example: The main body of the chart has John Smith---Ann Brown James Smith Arthur Smith
and a sub-tree has Ann Brown and her ancestors. Select all the members of Ann Brown's sub-tree by clicking on them with the Ctrl key held down. Drag them to be adjacent to John Smith. Drag John Smith---Ann Brown so that they switch positions.
You may or may not be successful, but it should at least provide many hours of entertainment.