OK. This helps a lot. I see a couple of issues. First, you’re trying to use the slicer like CAD. Yes, it can be done but it’s definitely the most self punishing way to go about affecting a model modification.
Second, you’ve got 18 disks that someone got misoriented. These are just in random order. This was likely due to you using the rotation tool and having rotated the object in the Y or X axis. Either way, start over.
Here’s what I found when I isolated the disks.

A hodgepodge mess of misoriented disks.
I realized that with this many disks, you must have spent a lot of time trying to orient them. There’s no point in fixing this. Start over it will be quicker.
Third, I’m guessing you’re trying to embed 18 6x2mm round magnets into your model. Your model is only 3.3mm in height. Trying to add a 2mm thick magnet will not end well, but try it out on single piece with only four magnets to see for yourself.

_________________________________________________________________
How to:
So having said that. How should you approach this assuming you still want to move forward with 18 individual magnets?(this was a painful to do as it was to post but I know of no shortcuts outside of CAD)
- Clone the object onto a new plate and delete everything but the Black circle. This will be used in a moment to create a template.
- Once you have that black circle on the new build plate. Make a disk primitive that is the size of your magnet. Then clone it as many times as you want. Click on Autoarrange and they will be distributed evenly in a square matrix
- Move the black circle off the plate temporarily. Switch back to the build plate with the magnet discs and draw rectangle around all of them using your shift key and mouse. This will lasso all of them into a single group.
- Move you round circle back to the build plate to use as a guide, center it and then start dragging the disks into an arrangement of your choosing.
- Delete the black circle you won’t need it after this.
- Lasso the magnetic circles that you just arranged. Right click and create and assembly. This will group them
7) Activate the build plate that has your model that you will add the magnets to.
8) Go back to the assembly of magnets on the other build plate, right click and hit center. It will center that assembly onto the build plate that is active.

9) After you’ve placed both assemblies on the build plate. Go to the object menu and Shift-click on each assembly, right click and click assemble.
10 Then go through each of the discs and change the type to negative.
Here’s what this looks like. I was not about to go through all 18 disks and I certainly wasn’t going to arrange them evenly. But I changed three of the disks to negatives and moved the slider to layer one to illustrate that it can be done. Just don’t touch the Z axis.
Cubs magnetized - example.3mf (248.9 KB)
__________________________________________
A better way.
Purchase self-adhesive magnetic sheet and cut it to the disk size and stick it onto the back of the model. It will be far cleaner and definitely a lot less expensive that 6mm magnets.
https://www.amazon.com/s?k=self+adhesive+magnetic+sheet