Hi Hatice. I've moved your question to the PADS community where it should get a quicker response.
Are you creating an integrated project (with a central library) or a netlist project? The output window that is cropped looks like a netlist, but it also looks like PADS 9.4 which doesn't have integrated project -- so the image has conflicts that may not have anything to do with your issue.
Are there any netlist or packaging errors in PADS Designer (aka xDxDesigner depending on version)?
If you open the prj file (with an ASCII editor) what does the FlowType KEY say? If it doesn't say KEY FlowType "PADS" it isn't a PADS Integrated project. We can't just change this value, but it should help determine the next steps.
I'm creating a netlist project, and using version .2. Not sure why it says 9.4