A series of MnxZn1-xO (x = 0.03, 0.05) nanostructures have been grown via the solution based chemical spray pyrolysis technique. Electron beam induced modifications on structural, linear and nonlinear optical and surface morphological properties have been studied and elaborated. GXRD (glancing angle X-ray diffraction) patterns show sharp diffraction peaks matching with the hexagonal wurtzite structure of ZnO thin films. The upsurge in e-beam dosage resulted in the shifting of XRD peaks (101) and (002) towards lower angle side, and increase in FWHM value. Gaussian deconvolution on PL spectra reveals the quenching of defect centers, implying the role of electron beam irradiation regulating luminescence and defect centers in the nanostructures. Irradiation induced spatial confinement and phonon localization effects have been observed in the films via micro Raman studies. The later are evident from spectral peak shifts and broadening. Detailed investigations on the effect of electron beam irradiation on third order nonlinear optical properties under continuous and pulsed mode of laser op-eration regimes are deliberated. Third order absorptive nonlinearity of the nanostructures evaluated using the open aperture Z-scan technique in both continuous and pulsed laser regimes shows strong nonlinear absorption coefficient βeff of the order 10 -4 cm/W confirming their suitability for passive optical limiting applications under intense radiation environments. Laser induced third harmonic generation (LITHG) experiment results supports the significant variation in nonlinearities upon electron beam irradiation, and the effect can be utilized for frequency conversion mechanisms in high power laser sources and UV light emitters.