For calibrating your printer, I always recommend https://teachingtechyt.github.io/calibration.html. Everything is step-by-step and helps teach you about the calibrations and what different settings do. I agree with the other commenter that you’re underextruding, based on your layers not filling in. Getting your E-steps calibrated is extremely important, then I’d start working on flow rates (which can change between rolls and brands)

You’ll want to google the exact steps for calibrating e-steps, but basically this is the setting that determines how many steps of the stepper motor are required to move the filament a given amount. You disconnect the bowden tube from the head, then push the filament through so a bit is exposed past the end of the tubing and mark exactly where the end of the tubing is on the filament. Now from your slicer you instruct the printer to extrude 100mm of filament, and very carefully measure how much actually comes out. If you have exactly 100mm then great, but typically you will find it off by a few mm (and in your case it’s probably less than 100mm). It doesn’t take much to cause a big problem. Any how-to page will show how you can read the current setting (I think it’s 92 steps by default), and there are formulas which will calculate the new number you need to change that to.

So the idea here is that if the slicer thinks it should be outputting 100mm of filament, but it only pushes 95mm instead, you won’t have enough filament to fill in the gaps. Setting the correct value on the printer will fix this, and then you can adjust more minor issues by changing the flow rate in the slicer. You will also note that different types or brands of filament extrude at slightly different rates, which is why your slicer may allow different profiles for the filament itself.

I’m not familiar with PrusaSlicer. Cura has always worked well for me, it’s free, and it provides quite a lot of options for fine-tuning your prints. If you find that Prusa doesn’t let you adjust the filament rate, give Cura a try.

You should only need to see a few layers to tell if there’s still a problem. No need to waste filament printing a complete failed piece.

Oh I should have mentioned in the previous post… if a cold-pull doesn’t make any difference, have you checked the nozzle itself? It’s a very tiny hole, easily damaged, so if the head smacked into anything it might have slightly crushed the tip (not something you would see by eye). You could also try clearing the nozzle with the long needle that came with the printer – if it doesn’t fit into the nozzle tip then it’s almost certainly suffered some damage. Always keep a bag of spare nozzles on hand!

I personally like https://teachingtechyt.github.io/calibration.html for all of the above. It provides gcode and stl files based on your input. I’ve had great success using it for my Ender 3.

Ignore all the stuff that says Klipper. Install the program called pronterface and then hook up your printer to your computer with USB. You can then run the commands the guide tells you.

You should really figure out how to calibrate the esteps if you never have before, it’ll save you a headache. This tutorial is a good visual: https://youtu.be/6PL_rSPZ3M8

To do the e-step process on your ender 3, you would need to open your favorite notepad application, copy/paste the g-code on that site, save the text file as .gcode, and get that g-code to your ender 3 (SD card, etc).

The same is true for the extrusion multiplier test - you would set the test up in your slicer, slice it, and then print. Some slicers, like orca slicer and super slicer, have a built in extrusion multiplier test that makes it very easy to do this.