Which camera are you using, iSTAR or iris360? If it's iris360 and it's serial number is 3000 or higher then use a tripod with a ball head and not one with pan/tilt arms.
You can then use the "pinch" option to edit out the area where the tripod is, but that's only a small area anyway.
There are other ways to completely remove the tripod using photoshop and a plugin called "super rune": http://www.superrune.com/tools/supercubic.php
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