Using a water jet can be a pain with small objects, during our testing phase we tried to find better ways to clean them using holders and what not help for sure but the best way to clean them for us has been with ultrasonic and acid... Sodium Hydroxide diluted with water in a 10:1 water to Sodium Hydroxide works pretty good, we upped it to almost 50-50 and still worked but need to be more diligent. We used clear glass vials from acrylic paints to hold the solution, then we would initially soak the parts in water to help remove the big chunks by hand, then soak it in the solution for 10 min in the ultrasonic. Once that is done IMMEDIATELY empty it into a sink and thoroughly rinse with water. Scrub with a brush and some soap and final rinse and finished. A bit more tedious but worked really well for us.
**Side Note** Water and Sodium Hydroxide (Lye Crystals) causes an exothermic reaction and will produce a lot of heat... do not place parts to be washed into the solution until the solution has cooled so you do not distort the printed parts.
Here is a list of how we cleaned them to better organize what i wrote...
1. Mix solution of Sodium Hydroxide and Water in container, once fully dissolved let stand for 5-10 min
2. Soak parts in water to loose support material and remove as much as possible by hand.
3. Place parts into Sodium Hydroxide solution and place in ultrasonic for 10 min. Room Temp
4. Remove parts and immediately immerse in running water to dilute any residual acid on parts.
5. Scrub parts with brush (We used a toothbrush) with soap and water.
6. Dry and viola
Hope this helps, this was the best we could find in our testing. All stratasys models have a super thin layer of support material hybrid where the support meats the model and soaking in water or anything wont remove this, however the acid soak will dissolve this. (Straight from stratasys support)