Animal behavior is governed by brain activity distributed and coordinated across multiple regions. Parallel progress in optical microscopy and the development of genetically encoded calcium indicators has advanced experimental approaches in systems neuroscience to assess brain activity simultaneously in multiple brain regions. Here, we provide a brief overview of optical recording techniques at this mesoscale level and of their combination with genetically encoded sensors and actuators. Next, we focus on the novel opportunities offered by extending fiber photometry to many brain regions, using compact arrays of optical fibers targeted to specific subnetworks of brain regions. We provide a detailed description and construction guidelines of high-density fiber array implants, including step-by-step surgical procedures for implantation and extraction. We describe several types of experiments enabled by this approach and highlight specific examples. We also discuss the challenges for analysis and interpretation of such mesoscopic recording data. Finally, we outline potential future improvements in terms of further functionalization of the multisite neural interfaces and of making them even less invasive.