CGI was actually fairly common practice by the 1990s, a watershed period for digital visual effects. Most prominently rendered in wireframe in the 1970s (Star Wars IV, 1977; Superman, 1978), by the mid-80s various scifi and fantasy films employed photoreal mapping effects (Flight of the Navigator, 1986) and were making strides in live action/digital composition and character animation (The Abyss, 1989). We tend to think of CGI in terms of photoreal humans or animals, which look dated by 2010s standards, but accepting that subtler blends of environmental digital VFX were quite common by then, and the industry's relative mastery of green or blue screen compositing and rotoscope animation by that time, it's not difficult to imagine that shots like the nail color change in Total Recall were done digitally. 

(The VFX team of Total Recall [won the Special Achievement Award for Visual Effects in 1990][1] for groundbreaking [use of CGI][2] as well as a mix of animatronics, stop motion and miniature set composites.)

That said, I would also accept that the nail color change is simple green screen and rotoscope animation, because of said mastery. Either way, based on the conspicuously saturated blue/orange of the nails, it's most likely the actresses's nails were painted green, making it easy to overlay any solid color in post-production. 

  [1]: http://www.imdb.com/title/tt0100802/awards
  [2]: http://www.youtube.com/watch?v=EsTza718oN0