Lido,

When CAESAR II provides the PCF, click Edit PCF. Replace all occurrences of FLBL with FLWN , and replace all occurrances of VVBW with VVFL.

This should get you what you want. Those blank flanges will appear as weld neck flanges and the flanges on the valves (now flanged valves as opposed to the original welded valves) will be properly oriented.

I believe you will find this to be the default settings in the next version of CAESAR II (2019 - in beta testing now).