Microbial activity will release large molecule organic molecules, such as, fatty acids and lipids. These organic molecules with hydrophilic heads and hydrophobic tails will affect crystallization of minerals in crystal shape, microstructure, and even crystal structures. Our results from both laboratory synthesized and natural magnetite in modern soil and palesol show nano-meter scale worm-hole-like pores. These pores are directly related to self-assembling and templating of the organic molecules. Calcite "crystals" consisted of nano-pores and calcite nano-crystals can be formed when the organic molecules exit. The calcite formed may display cube-le and even flower-like shapes. According to our results, such kinds of calcite crystals do not have to be replacement products of microbes. However, they indicate presence of the organic molecule released from microbes. Unique nano-porous structures and shapes can be formed based on silica component when the organic components exit. Mineral shapes that are different from inorganically crystallized crystals can be formed in the presence of particular organic molecule. They do not have to be replacement of microbes and take the pseudomorphs of microbes. However, such kinds of microstructures and morphologies can indicate presence of microbial activity. These indicators may be used for investigation of extraterrestrial microbial activities.