Hi Ade,
If you suspect you have lots of cellular contamination, you will want to purify your crude vesicles. There are many ways to purify EVs. Two common methods described in this paper are filtration and density centrifugation. Passing your apoplastic wash fluids through a 0.22 um filter will remove large cellular debris/organelles. Density centrifugation is another way to separate EVs away from other cellular components based on buoyant density (see section F). Ultracentrifugation itself is an excellent way to separate out organelles, if you know at which speed the organelles pellet.
However, the best way to remove cellular contamination is to avoid damaging the plants. Use younger (~5-6 weeks), healthy plants, and be gentle when extracting your wash.