Hi,
This is more or less a good workflow.
1. Align all your images. Once this SfM step is finished, you will end up with a sparse point cloud. The reprojection error for that chunck gives you the average and maximum value of all reprojection errors. Ideally, they should be lower than 1 pixel. So, now one can go and edit the point cloud;
2. Select points that are far away from the object you want to reconstruct. Now delete those points (better: select the object and some space around and delete - using the crop tool - all other points).
3. Go to Edit > Gradual selection and check how many points are selected when you drag the slider till about 1. If there are just a few hundreds till a few thousands of points, go ahead. Now the points with a reprojection error higher than 1 pixel are selected. Delete these points;
4. Now that you have a sparse point cloud containing only points with a reprojection error smaller than 1 pixel, optimize the point cloud (which runs a bundle block adjustment and also optimizes the camera parameters). When doing so, uncheck "Fit Aspect" and "Fit skew", since these are 0 in normal frame cameras.
Now, go to your chunck, right click and select "Show Info" to verify that the average reprojection error dropped. Most likely, there will again be points with an error higher than 1 (since all points and their reprojections are recalculated during the optimization step). You could start again from step 3 and make 1 to 2 more iterations until you are satisfied with the global accuracy.
As was already mentioned: never delete too many points, as image alignments can be broken. Never iterate too much: the accuracy values will become better and better, but your reconstruction will show ripples. Best is to optimize 1-3 times and try to get as little points as possible with a reprojection error surpassing 1.
Hope this helps. CU,
Geert