In recent years, there have been many studies on the growth characteristics of mammalian cells on 2D substrates. However, the growth environment of cells in vivo is mainly in 3D microenvironments, in which the cell growth behaviors are different from that in 2D substrates. Therefore, we could construct polymer-microtube-arrays as tubular 3D microenvironment for studying cell behaviors. An effective microoperating system based on microtube arrays was used for capture, transfer, and release of yeast, embryonic fibroblast mouse cells, and human breast cancer cells. The microtube arrays were used as transparent 3D yeast culture scaffolds to study the effect of 2D tubular confinement on the growth characteristics of budding yeast. The growth tendency and morphological characteristics of yeasts in the microtube was found to have a significant correlation with the diameter of the tubes. Especially in conical microtubes, the captured yeasts showed distinct asymmetrical growth tendency. We believe that this processing method combined with new biological materials has great potential in the area of cell biology and biological tissue engineering.