Ultrafast laser ablation is widely used as a versatile method for accurate micro-machining of polymers, glasses and metals for a variety of industrial and biomedical applications. We report on the use of a novel process parameter, the modulation of the laser pulse energy during the multi-scan texturing of surfaces. We show that this new and straightforward control method allows us to attain higher and lower roughness (Ra) values than the conventional constant pulse energy irradiation sequence. This new multi-scanning laser ablation strategy was conducted on metals that are commonly used in the biomedical industry, such as stainless steel, titanium, brass and silver samples, using a linear (increasing or decreasing) gradient of pulse energy, i.e., varying the pulse energy across successive laser scans. The effects of ablation were studied in terms of roughness, developed interfacial area ratio, skewness and ablation efficiency of the processed surfaces. Significantly, the investigation has shown a global trend for all samples that the roughness is minimum when a decreasing energy pulse sequence is employed, i.e., the irradiation sequence ends up with the applied laser fluences close to threshold laser fluences and is maximum with increasing energy distribution. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) analysis on single craters with the three different energy deposition conditions revealed a chaotic and random material redistribution in the cases of uniform and increasing energy distributions and the presence of regular laser-induced periodic surface structures (LIPSS) at the bottom of the ablation region in the case of decreasing energy distribution. It is also shown that the ablation efficiency of the ablated surfaces does not significantly change between the three cases. Therefore, this novel energy control strategy permits the control of the roughness of the processed surfaces without losing the ablation efficiency.