With the growth in the diversity of novel molecular communication via diffusion-based (MCvD) applications, the term synchronization can entail different technologies in MCvD-based nanonetworks - from relatively simple collaborative actions to complex symbol timing recovery. Motivated by the need for distinction or uniformity in the technologies, we introduce the notion of timing alignment, which is an umbrella term that includes any element that enables nanomachines to execute processes or actions in an organized manner. Four elements of timing alignment are identified, namely, hardware, protocol, network, and application. In a tutorial manner, the elements are described both at the microscopic level (as individual elements) and at the macroscopic level (as collective elements). A combination of existing and new knowledge is used to elicit the challenges that lie in the path of the development of MCvD-based medical systems. Timing alignment can therefore be approached either as a single topic or by its elements.