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Multiplexed patterns of hydrogels and phospholipids with fluorescent dyes are accomplished by dip-pen nanolithographyÂ® (DPNÂ®). For example, four different dyes-labeled hydrogel dot arrays are DPNÂ® patterned within 50 Ã 50 Â¿m2 area, and two different dyes-doped phospholipids dots and letters with less than 1 Â¿m line-width are also DPNÂ® patterned. We demonstrate that multi-ink patterns with precise alignment are able to be printed by DPNÂ® within a micron-scale. Moreover, this multi-ink DPNÂ® patterning methodology can be extended to delicate bio-materials printing in a subcellular scale with accurate positioning control.