In this paper, the power quality of multi-area microgrids is addressed. For this, Active Power Filters (APFs) and Distributed Generators (DGs) inverters are used. To achieve the reference value of power quality indices of different areas, a strategy based on cooperation between DGs and APFs is proposed. Hierarchical control is applied to control DGs inverters and APFs in a coordinated way. Primary control consists of power droop controller of DGs, selective virtual impedance and voltage/current regulators. Based on the secondary control, voltage compensation of Points of Common Coupling (PCCs) of multi-area microgrid is carried out by DGs. Voltage compensation of PCCs by DGs may cause violation from maximum allowable voltage distortion at DGs terminals. Thus, tertiary control is used to mitigate these violations by using APF in proper coordination with secondary control. Evaluation of the proposed hierarchical control is carried out by simulation.