A system for cutting a flap in the cornea of an eye using polarization sensitive optical coherence tomography (PS-OCT), comprising: a PS-OCT system comprising: a PS-OCT source operable to generate a PS-OCT source beam; a polarization component operable to control a polarization of the PS-OCT source beam; a reference reflector; a beam splitter operable to split the PS-OCT source beam into a sample beam that travels along a sample arm until it is reflected by a sample in the cornea of the eye to form a reflected sample beam, and a reference beam that travels along a reference arm until it is reflected by the reference reflector to form a reflected reference beam, and operable to combine the reflected sample beam and the reflected reference beam to form a reflected PS-OCT beam; a wave plate operable to convert the sample beam into polarized light with a known polarization state such that a polarized sample beam is incident upon the sample; a detector operable to receive the reflected PS-OCT beam, detect an interference pattern of the reflected PS-OCT beam, and generate data relating to the interference pattern; and a femtosecond laser operable to generate a photodisruption pattern to cut a flap in the sample, and connected to a control device operable to adjust the photodisruption pattern generated by the femtosecond laser; and a processor operable to: receive data relating to the interference pattern of the reflected PS-OCT beam; generate a control signal; and transmit the control signal to the control device connected to the femtosecond laser, characterized in that the processor is further configured to: determine a relative fiber orientation of the portion of the sample reflecting the sample beam, based on a birefringence property of the portion of the sample; determine whether the photodisruption pattern should be adjusted horizontally or vertically based on the relative fiber orientation of the portion of the sample; and generate the control signal operable to adjust the photodisruption pattern horizontally or vertically when it is determined that the photodisruption pattern should be adjusted. a PS-OCT system comprising: a PS-OCT source operable to generate a PS-OCT source beam; a polarization component operable to control a polarization of the PS-OCT source beam; a reference reflector; a beam splitter operable to split the PS-OCT source beam into a sample beam that travels along a sample arm until it is reflected by a sample in the cornea of the eye to form a reflected sample beam, and a reference beam that travels along a reference arm until it is reflected by the reference reflector to form a reflected reference beam, and operable to combine the reflected sample beam and the reflected reference beam to form a reflected PS-OCT beam; a wave plate operable to convert the sample beam into polarized light with a known polarization state such that a polarized sample beam is incident upon the sample; a detector operable to receive the reflected PS-OCT beam, detect an interference pattern of the reflected PS-OCT beam, and generate data relating to the interference pattern; and a PS-OCT source operable to generate a PS-OCT source beam; a polarization component operable to control a polarization of the PS-OCT source beam; a reference reflector; a beam splitter operable to split the PS-OCT source beam into a sample beam that travels along a sample arm until it is reflected by a sample in the cornea of the eye to form a reflected sample beam, and a reference beam that travels along a reference arm until it is reflected by the reference reflector to form a reflected reference beam, and operable to combine the reflected sample beam and the reflected reference beam to form a reflected PS-OCT beam; a wave plate operable to convert the sample beam into polarized light with a known polarization state such that a polarized sample beam is incident upon the sample; a detector operable to receive the reflected PS-OCT beam, detect an interference pattern of the reflected PS-OCT beam, and generate data relating to the interference pattern; and a femtosecond laser operable to generate a photodisruption pattern to cut a flap in the sample, and connected to a control device operable to adjust the photodisruption pattern generated by the femtosecond laser; and a processor operable to: receive data relating to the interference pattern of the reflected PS-OCT beam; generate a control signal; and transmit the control signal to the control device connected to the femtosecond laser, characterized in that the processor is further configured to: determine a relative fiber orientation of the portion of the sample reflecting the sample beam, based on a birefringence property of the portion of the sample; determine whether the photodisruption pattern should be adjusted horizontally or vertically based on the relative fiber orientation of the portion of the sample; and generate the control signal operable to adjust the photodisruption pattern horizontally or vertically when it is determined that the photodisruption pattern should be adjusted. determine whether the photodisruption pattern should be adjusted horizontally or vertically based on the relative fiber orientation of the portion of the sample; and generate the control signal operable to adjust the photodisruption pattern horizontally or vertically when it is determined that the photodisruption pattern should be adjusted.