Fragmentation and isomerization of methylamine (CH3NH2+), methanol (CH3OH+), and methyl fluoride (CH3F+) cations by short, intense laser pulses have been studied by ab initio classical trajectory calculations. Born-Oppenheimer molecular dynamics (BOMD) on the ground-state potential energy surface were calculated with the CAM-B3LYP/6-31G(d,p) level of theory for the cations in a four-cycle laser pulse with a wavelengths of 7 mu m and intensities of 0.88 X 10(14) and 1.7 X 10(14) W/cm(2). The most abundant reaction path was (CHX+)-X-2 + H (63-100%), with the second most favorable path being HCX+ + H-2 (0-33%), followed by isomerization to CH2XH+ (0-8%). C-X cleavage after isomerization was observed only in methyl fluoride. Compared to random orientation, CH3X+ with the C-X aligned with the laser polarization gained energy nearly twice as much from laser fields. The percentage of CH3+ + X dissociation increased when the C-X bond was aligned with the laser field. Alignment also increased the branching ratio for H2 elimination in CH3NH2+ and CH3OH+ and for isomerization in CH3OH+.