"The week's been fantastic. Qualifying and beating a top-ten player is a big positive and I have to remember that."
Baltacha, the world number 65, recorded a first-serve percentage of 33% in the first set as Molik converted all three break points on offer.
The Briton fell two breaks down early in the second set before eventually holding serve twice but Molik strolled to the win.
Molik plays China's Zheng Jie, who beat Russia's Maria Sharapova 6-3 2-6 6-3 in a match of dropped service games.
Zheng was broken six times, but she hit back with seven breaks of her own as Sharapova, the 2006 winner, struggled with an injury to her right elbow and had 14 double faults.
The number 10 seed lost the last four games after getting treatment while leading 3-2 in the deciding set and preparing to serve.
Elsewhere, second seed Caroline Wozniacki of Denmark had no problems in a routine 6-0 6-3 victory over Maria Kirilenko of Russia.
In other matches, Poland's fifth seed Agnieszka Radwanska beat Gisela Dulko of Argentina 6-1 6-0, while France's 11th seed Marion Bartoli beat Jill Craybas of the USA 6-2 6-0.
But 15th seed Francesca Schiavone of Italy fell 6-7 (7-4) 7-6 (7-2) 6-4 to France's Aravane Rezai in a match that stretched just short of three hours.
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