Choose the Delete Holes command 
.
On the command bar do one of the following:
Set the Single option, select the cylindrical or conical faces you want to delete, then click the Accept button.
Set the By Operator option, type a value that represents the largest hole you want to delete. All holes that are less than or equal to this value are highlighted.
On the command bar, click the Preview button.
On the command bar, click the Finish button.
Tip:
When you use the Single option, you can select the faces individually or you can drag a fence to select a group of faces.
You can delete holes on the design model or you can delete holes to create a simplified version of the model in the Simplify Model environment.
The holes you delete in the Simplify Model environment are added to the Simplify section of PathFinder.
You can use the commands on the shortcut menu to edit, delete, suppress, and rename the simplified features you define.