Contours keeps including trees and foliage

Of course, if you have too many trees you won't be able to see the ground, but since your point cloud is classifying correctly that probably isn't the problem. When I create seeds as the first step of ground extraction, I then cut a vertical section through the mesh and move it across the entire site looking for seeds in the trees or under ground. I erase them and then run final ground extraction. Hope that helps. 

I do have rather large clumps of trees in my area of interest. Is there an online guide somewhere to your process? I don't know how to create sections or move them. I tried to create seeds in a ground extraction, but it didn't let me see them or edit them first.

So I'm wondering if there is an online tutorial or guide that showcases your process. It seems to be the way foreward.

Thanks for the help.

There are some tutorials:

www.youtube.com/results

Yea, photogrammetry isn't LiDAR. Trees are tough. However, here are some steps for working around them as best as possible.

1 - Set up a level for Seeds. I use red and make the line weight heavy, like 8, so the seeds are easy to see.

2 - Open the Reality Modeling workflow and click on Ground Extraction (If you can't find a particular tool just use the search feature at the top of the ribbon)

3 - In the Ground Extraction dialog box set the Seed mode to Automatic, click on the measuring stick  and use that tool to measure the smallest side of the largest structure, if you have one. For Output select Seeds and set the level to your Seed level. You can uncheck the boxes for point cloud, etc this time around. Follow the prompts to identify the reality mesh and accept. It'll think for a minute and then you should see a bunch of red dots. Some of them will be in your trees. Most should be on the ground.

4 - Open the Section tool dialog box (use the search if you don't know where it is). In the second row of tools pick the vertical section tool, click on Thickness and set it to some reasonable thickness like 10'. (This kind of depends on how big your site is) Below that set your Forward/Backward Step to be something a little smaller than your section thickness. That will make sure that you have seen everything as you move your section forward. Go to a top view and follow the prompts to pick a first and second point that span your site and are at one end of the site. The Create Section Wizard will open. Choose a target view for your section to show in.

5 - You should have a top view open that shows your section spanning your site and your Section target view open showing that 10' slice that you made. You'll see lots of seeds in the plan view and whatever seeds are contained within the section in that target view. If any seeds are up in a tree or underground use a right crossing selection to select and then delete them.

6 - Open the Reality Modeling Presentation tool box. (I like to keep it docked on the side) At the top, in the row of icons there are 2 sets of feet in the middle. One moves your section forward, the other backward by the amount that you told it to when you set up the section. Keep moving your section through your site removing bad seeds from the trees etc. You can also copy a seed and paste it onto any ground that you can see between your trees.

7 - Once you've cleaned the errant seeds from your whole site, go back and do Ground extraction again. This time instead of picking the Automatic Seed Mode, pick Points and make sure that the Level is set to seeds. The Automatic makes it's best guess at what ground is. Once you've cleaned up the seeds you can let the tool use them to find the ground. Under the Output you can turn on the point cloud, terrain and mesh. Accept and save your tin, stm, 3sm and pod. When its done running all of those products should be attached to your drawing and it'll look like a mess. You can turn off the Seeds level.

8 - To see just the mesh, turn off the Reality Model view. Open up your Scalable Terrain Model dialog box. Down at the bottom, next to the view control boxes are some icons. One is Display mesh and another is Display Contours. Toggle them on and off. If you select the model and go to properties you'll see your STM. Open the tree and click on Calculated Features>Contours. With Contours selected you can turn on smoothing, change the contour intervals, etc.  If you click on the Major or Minor contours it'll let you put them onto new levels, change the colors, add text and other fun stuff. Hopefully you had enough ground around your trees for the tool to estimate the contours under them.

Hope this helps.