Pectin, which is made from citrus peel and waste, is one of the most used compounds in the food industry. For large-scale production, a combination of membrane-vacuum filtering has been suggested as an alternative to traditional methods of purifying the acidic solution for pectin extraction. This study investigates the main factors involved in the membrane filtering system for the separation of fibrous materials from an acidic pectin solution under a vacuum. These factors include filter-aid-particle size, amount of filter-aid (perlite) added to the solution, and the vacuum level, effect, separation quality, volumetric flow rate, and energy consumption. A vacuum separation device was developed for this purpose in order to separate the fibrous material dissolved in the solution. The independent variables were examined at three levels, the data were analyzed, and the optimum value for each variable was determined using the response surface method (RSM). Results revealed that increasing the vacuum level from 0.2 to 0.4 bar increases the flow rate 6.5 folds, while, a further increase in the vacuum level decreases the flow rate. This indicates clogging of the paper filter and decreased flow rate at a vacuum level of 0.6 bar and perlite particle size of 100 microns. The evaluation results showed that the thickness of the perlite layer has the greatest effect on the separation efficiency and when increased from 1 to 2 cm, increases the efficiency 2.5 folds. The maximum value of separation efficiency was obtained at a vacuum level of 0.2 bar, particle size of 20 microns, and perlite thickness of 2 cm. The energy consumption of 60-micron perlite was 0.74 Wh in the optimal state, and the larger and smaller sizes of perlite had 4.5 times the energy consumption. These findings are applicable in the industrial-scale implementation of a biomaterial separation system using vacuum membrane filtering.