Nonoy,
Mabuhay! If I understand your question, you have tried to use a GTAW root pass in a stainless steel pipe weld, but it did not penetrate completely through the joint and you had to backgouge and reweld from the inside of the pipe. The joint geometry should have a 37-1/2 degree bevel angle on each side (75 degrees total). The root opening should be 3/32 in. to 1/8 in. and about 1/16 in. land on the end of the bevel. Use a 3/32 in. or 1/8 in. diameter filler wire, depending on the root opening and feed it into the puddle at the root. Here is an illustration that may help:
http://www.tpub.com/content/construction/14250/css/14250_51.htm