Cortex and hippocampus are relatively easy to micro-dissect and I don't see why you should affect integrity.

What I see is that you will have a hard time when cutting due orientation and deformation issues because you won't have the structural support of the other brain structures that also help during orientation, providing good landmarks. 

So the first question IMHO is, dear Kpobari: 

so you need a fixation of brain tissue first:   either chemically or chemically-physically.

i) perfusion (mild*) or classical**)) fixation - opening of skull/cranial vault, oriented [and standardized] dissection / excision of the area of interest with perhaps a self-made cutting tool - followed by additional immersion fixation - Paraffin embedding - IHC-staining etc.

ii) at least after perfusion (mild*) fixation excise brain area, wash in suited buffer, immerse in 10,20,30% (or more) sucrose solution (as cryoprotectant) and freeze accordingly (-25°C in a cryostat [not recommended but may be sufficient], or at least minus -80°C) -then cryosectioning.

Right Orientation or 'oriented sectioning' (if you need such) - as David said - may be "hard time", but if you imagine the rat's anatomical "facts" (e.g. find Fig.4. in :https://www.researchgate.net/publication/5405996_Mossy_fiber_sprouting_in_pilocarpine-induced_status_epilepticus_rat_hippocampus_A_correlative_study_of_diffusion_spectrum_imaging_and_histology/figures?lo=1)  you could easily find your section plane by overview staining [ H&E, Nissl stain, CV ] of selected sections. 

Performing a Google-search (or other Search machine) for e.g.: 

" RAT AND hippocampus region AND 'Commissura anterior' AND 'Corpus Callosum' map OR ATLAS "   reveals a lot of valuable sources and literature worth at least to be shortly view if not read.

*) Mild fixation:  e. g. PLP-fix (NAKANE

**) Classical fixation: for preservation of morphology usually combination of aldehydes(e. g. FA+GA in PO4-buffer, caution: special treatments/application modes, recipes & schedules [may]apply!) or solely suitably buffered FA (better PFA)-solutions

Best wishes and good luck, WM

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