3D Systems, he said, featured a broader product line and a very aggressive acquisition strategy.
"It might turn out to be that's the right thing to do in a couple of years, but for now we think Stratasys is the better play, sells at a discount, should sell at a premium to 3-D, in our view," he said.
Stratasys appears on track to post earnings growth of 18 percent this year, Milunovich said.
Milunovich, who is managing director of the U.S. Research Group at UBS, has been ranked the No. 1 IT hardware analyst for 12 consecutive years by Institutional Investor magazine.
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The expected entrance of Hewlett-Packard later this year into the sector would be good for 3-D printing, he added.
"It's a fragmented market. I think there's a lot of room for a lot of folks to succeed," he said. "And I would argue at this early stage, while they may be very competitive and take some share, I think it's more important to legitimize the market, as they say."
Disclosure: UBS holds no position in 3D Systems, Stratasys, ExOne or Hewlett-Packard. Hewlett-Packard was a client of UBS in the past 12 months.
—By CNBC's Bruno J. Navarro.