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We present mapping results of two prestellar cores, L1544 and L694-2, embedded in filamentary clouds in C$^{18}$O (3-2), $^{13}$CO (3-2), $^{12}$CO (3-2), HCO$^+$ (4-3), and H$^{13}$CO$^+$ (4-3) with the JCMT telescope to examine the role of the filamentary structures in the formation of dense cores in the clouds, with new distance estimates for L1544 ($175_{-3}^{+4}$ pc) and L694-2 ($203_{-7}^{+6}$ pc). From these observations, we found that the non-thermal velocity dispersion of two prestellar cores and their surrounding clouds are smaller than or comparable to the sound speed. This may indicate that the turbulence has already been dissipated for both filaments and cores during their formation time. We also found a $λ/4$ shift between the periodic oscillations in the velocity and the column density distributions implying the possible presence of gravitational core-forming flow motion along the axis of the filament. The mass accretion rates due to these flow motions are estimated to be 2-3 M$_\odot$ Myr$^{-1}$, being comparable to that for Serpens cloud but much smaller than those for the Hub filaments, cluster, or high mass forming filaments by 1 or 2 order of magnitudes. From this study, we suggest that the filaments in our targets might be formed from the shock-compression of colliding clouds, and then the cores are formed by gravitational fragmentation of the filaments to evolve to the prestellar stage. We conclude that the filamentary structures in the clouds play an important role in the entire process of formation of dense cores and their evolution.