The microfossils taxonomy, apart from the recently and thoroughly studied molecular data is mostly based on the morphology of their external shape. Classical microfossil studies involve the usage of an optic microscope in order to identify the external morphological characters, followed by detailed examination using Scanning Electron Microscopy (SEM). In many cases, for an accurate determination of the specimen, correlation of the characters from its opposite sides is necessary. Using 2D images in the determination process is quite hard and often could lead to poor and insufficient information gathering. This study presents a new method for the microfossil representation. The method allows a more accurate measurement of the morphology of the specimens. The “Structure-from-Motion” Photogrammetry technique makes use of a very accessible methodology: SEM photos and photogrammetry software. The 3D models have been made for nine specimens of foraminifera, ostracods, radiolarians, ascidian spicules, and a dinoflagellate cysts. The variability of the studied specimens proves that this method can be successfully applied to almost all groups of microorganisms.