Using clearFocus() didn't seem to be working for me either as you found (saw in comments to another answer), but what worked for me in the end was adding:
<LinearLayout
android:id="@+id/my_layout"
android:focusable="true"
android:focusableInTouchMode="true" ...>
to my very top level Layout View (a linear layout). To remove focus from all Buttons/EditTexts etc, you can then just do
LinearLayout myLayout = (LinearLayout) activity.findViewById(R.id.my_layout);
myLayout.requestFocus();
Requesting focus did nothing unless I set the view to be focusable.