Prep work is essential to a good finish. If you don't do the prep, then you will certainly not get a nice smooth finish on top of your surface. The primers and paint magnify the imperfections, unless you pour finish on your project.
You can sand out the rough spots if they are raised wood fibers and recoat. But if the surface was improperly cleaned to be free of dirt, dust, sanding dust, etc., and it is trapped in the primer and paint I would sand all of it off and start over.
Wait a few days before sanding to allow the paint to cure a bit and to keep from simply rolling up the latex and making your surface even rougher. The fresh latex will easily scratch with sandpaper, leaving behind grooves that will show in your subsequent coats of paint.
If you sand off the primer and paint, be careful with your prep; sand your primer as needed and make sure it is glass smooth and clean before applying finish.
Too late to do what I do. On all wood projects that will be painted I use sanding sealer first then sand to very smooth. Then primer and paint. Makes a very smooth finish. WW
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