One way to process these isolated faces (shown in Fig. 1) is to first isolate a part of face in blender. The key binding is Alt+H. Now, we can zoom in to do more detailed manipulation in this region.

Figure 1: There are many isolated faces.

Figure 1: There are many isolated faces.

Figure 2: You can isolate a part of region by Alt+H in Edit mode

Figure 2: You can isolate a part of region by Alt+H in Edit mode

Now, after clean, we arrive at a very big hole as shown in Fig. 3. We need to merge this big hole in the next step.

Figure 3: A big hole after the votex, edge, and face clean.

Figure 3: A big hole after the votex, edge, and face clean.

Tips: Delete edges

Just click the middle blue button in Fig. 4.

Figure 4: To select edges, you need to click on the middle blue button.

Figure 4: To select edges, you need to click on the middle blue button.

You can click the middle and right buttons at the same time to select the edge and the face at the same time.